Adding Normalization step to WF (CLAHE) by dianichj · Pull Request #1256 · galaxyproject/iwc

dianichj · 2026-06-10T15:21:53Z

Added a normalization step to the workflow

Update Workflow Version

github-actions · 2026-06-10T17:18:28Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ histological-staining-area-quantification.ga_0

Problems:

Output with path /tmp/tmp01exxr29/Compute on dataset 150__2c71f1e3-c5eb-4446-85c5-7f88607773d3.tabular different than expected
Expected text matching expression 'treatment_3\t255\t0\.003576[0-9]+\t10607\.0\t10678\.0\t360000\t2\.946[0-9]+' in output ('sample_id	label	mean_intensity	area	area_filled	total_area	percent_area
control_1	255	0.5279595851898193	1817.0	1850.0	360000	0.5047222222222222
control_2	255	0.583838164806366	3177.0	3249.0	360000	0.8825
control_3	255	0.5820612907409668	784.0	792.0	360000	0.21777777777777776
treatment_1	255	0.0017691614339128137	3720.0	3720.0	360000	1.0333333333333332
treatment_2	255	0.0018343921983614564	3804.0	3804.0	360000	1.0566666666666666
treatment_3	255	0.0014414299512282014	5156.0	5156.0	360000	1.4322222222222223
')

Output with path /tmp/tmpkzjayqbe/Extract image features__289abc59-99db-4017-9c3e-59ea26559cd2.tabular different than expected
Expected text matching expression '255\t0\.61[0-9]+\t1888\.0\t1902\.0' in output ('label	mean_intensity	area	area_filled
255	0.5279595851898193	1817.0	1850.0
')

Workflow invocation details

Invocation Messages

Steps

Step 1: ROI image for staining analysis:
- step_state: scheduled

Step 2: Sample ID (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:9.5
```

Command Line:

times=1; yes -- 'sample_id' 2>/dev/null | head -n $times >> '/tmp/tmpvdrzu6zl/job_working_directory/000/7/outputs/dataset_75f8cfc6-da64-4025-9150-e7c6b31c333f.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "sample_id", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 3: header for total area (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:9.5
```

Command Line:

times=1; yes -- 'total_area' 2>/dev/null | head -n $times >> '/tmp/tmpvdrzu6zl/job_working_directory/000/8/outputs/dataset_4bbe0e5f-52d3-4d27-8e28-b233cfec92cd.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "total_area", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 4: Stain intensity normalization (CLAHE) (toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.25.2+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-cda17ae6e704c03b90ac5363e2f0d2e9541adcca:ee074f2ad5d1ed14cc80d11e4b522450e77523e9-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpvdrzu6zl/files/8/2/4/dataset_8245d9e0-f480-4825-bb08-cb111774aa8e.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/12/outputs/dataset_bf713c43-7324-497f-bccc-02ef5afd941d.dat' clahe

Exit Code:

```
0
```

Standard Error:

/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py:32: FutureWarning: The plugin infrastructure in `skimage.io` and the parameter `plugin` are deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not use the parameter `plugin`. Instead, use `imageio` or other I/O packages directly. See also `imsave`.
  skimage.io.imsave(args.out_file.name, res, plugin="tifffile")

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
h_type	`"clahe"`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-cda17ae6e704c03b90ac5363e2f0d2e9541adcca:ee074f2ad5d1ed14cc80d11e4b522450e77523e9-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpvdrzu6zl/files/c/6/7/dataset_c6747ab6-c9e1-44d3-931f-c2b7aa410fcf.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/9/outputs/dataset_bb0bd6e3-1e9f-4b10-93b6-aa0312d1ae6c.dat' clahe

Exit Code:

```
0
```

Standard Error:

/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py:32: FutureWarning: The plugin infrastructure in `skimage.io` and the parameter `plugin` are deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not use the parameter `plugin`. Instead, use `imageio` or other I/O packages directly. See also `imsave`.
  skimage.io.imsave(args.out_file.name, res, plugin="tifffile")

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
h_type	`"clahe"`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-cda17ae6e704c03b90ac5363e2f0d2e9541adcca:ee074f2ad5d1ed14cc80d11e4b522450e77523e9-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpvdrzu6zl/files/9/6/e/dataset_96efabb1-40f6-4819-aa95-2c02d2d436a9.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/10/outputs/dataset_a7f6f446-ac3a-4060-8f73-2a68b7a1a36e.dat' clahe

Exit Code:

```
0
```

Standard Error:

/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py:32: FutureWarning: The plugin infrastructure in `skimage.io` and the parameter `plugin` are deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not use the parameter `plugin`. Instead, use `imageio` or other I/O packages directly. See also `imsave`.
  skimage.io.imsave(args.out_file.name, res, plugin="tifffile")

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
h_type	`"clahe"`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-cda17ae6e704c03b90ac5363e2f0d2e9541adcca:ee074f2ad5d1ed14cc80d11e4b522450e77523e9-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpvdrzu6zl/files/3/1/0/dataset_31042e91-87c9-4c8b-aaf3-af5bac32c8a0.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/11/outputs/dataset_ec6e2e14-ce7e-4f8c-b9bd-4d75c6336dd4.dat' clahe

Exit Code:

```
0
```

Standard Error:

/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py:32: FutureWarning: The plugin infrastructure in `skimage.io` and the parameter `plugin` are deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not use the parameter `plugin`. Instead, use `imageio` or other I/O packages directly. See also `imsave`.
  skimage.io.imsave(args.out_file.name, res, plugin="tifffile")

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
h_type	`"clahe"`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-cda17ae6e704c03b90ac5363e2f0d2e9541adcca:ee074f2ad5d1ed14cc80d11e4b522450e77523e9-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpvdrzu6zl/files/7/8/0/dataset_780cecc2-ea20-47c2-8890-a434a020efaa.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/13/outputs/dataset_719cb02f-772c-446d-aca0-55166a0eaaf2.dat' clahe

Exit Code:

```
0
```

Standard Error:

/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py:32: FutureWarning: The plugin infrastructure in `skimage.io` and the parameter `plugin` are deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not use the parameter `plugin`. Instead, use `imageio` or other I/O packages directly. See also `imsave`.
  skimage.io.imsave(args.out_file.name, res, plugin="tifffile")

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
h_type	`"clahe"`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-cda17ae6e704c03b90ac5363e2f0d2e9541adcca:ee074f2ad5d1ed14cc80d11e4b522450e77523e9-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpvdrzu6zl/files/6/1/5/dataset_6151cf18-5e29-4926-b5a1-c18e081f0bb9.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/14/outputs/dataset_13d1aecd-badd-41d3-a146-864850a26d45.dat' clahe

Exit Code:

```
0
```

Standard Error:

/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/99e0ef91ea5e/2d_histogram_equalization/histogram_equalization.py:32: FutureWarning: The plugin infrastructure in `skimage.io` and the parameter `plugin` are deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not use the parameter `plugin`. Instead, use `imageio` or other I/O packages directly. See also `imsave`.
  skimage.io.imsave(args.out_file.name, res, plugin="tifffile")

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
h_type	`"clahe"`

Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/5.7.1+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/bftools:5.7.1--hdfd78af_1

Command Line:

showinf '/tmp/tmpvdrzu6zl/files/3/1/0/dataset_31042e91-87c9-4c8b-aaf3-af5bac32c8a0.dat' -no-upgrade -minmax -nopix > '/tmp/tmpvdrzu6zl/job_working_directory/000/17/outputs/dataset_44d763bc-cfa8-4a54-ba93-1b71ddbabdef.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/bftools:5.7.1--hdfd78af_1

Command Line:

showinf '/tmp/tmpvdrzu6zl/files/8/2/4/dataset_8245d9e0-f480-4825-bb08-cb111774aa8e.dat' -no-upgrade -minmax -nopix > '/tmp/tmpvdrzu6zl/job_working_directory/000/18/outputs/dataset_82bf864c-56e4-4fcd-ac0a-1c52e50c4a4f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/bftools:5.7.1--hdfd78af_1

Command Line:

showinf '/tmp/tmpvdrzu6zl/files/c/6/7/dataset_c6747ab6-c9e1-44d3-931f-c2b7aa410fcf.dat' -no-upgrade -minmax -nopix > '/tmp/tmpvdrzu6zl/job_working_directory/000/15/outputs/dataset_3abcd0d8-a0cc-4e68-81ca-82971a0fbc94.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/bftools:5.7.1--hdfd78af_1

Command Line:

showinf '/tmp/tmpvdrzu6zl/files/7/8/0/dataset_780cecc2-ea20-47c2-8890-a434a020efaa.dat' -no-upgrade -minmax -nopix > '/tmp/tmpvdrzu6zl/job_working_directory/000/19/outputs/dataset_cbf91b36-d00c-4e91-a2ad-7d3d87b179f6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/bftools:5.7.1--hdfd78af_1

Command Line:

showinf '/tmp/tmpvdrzu6zl/files/9/6/e/dataset_96efabb1-40f6-4819-aa95-2c02d2d436a9.dat' -no-upgrade -minmax -nopix > '/tmp/tmpvdrzu6zl/job_working_directory/000/16/outputs/dataset_a27ce60c-3cfa-4751-a175-fc6e301c8df6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/bftools:5.7.1--hdfd78af_1

Command Line:

showinf '/tmp/tmpvdrzu6zl/files/6/1/5/dataset_6151cf18-5e29-4926-b5a1-c18e081f0bb9.dat' -no-upgrade -minmax -nopix > '/tmp/tmpvdrzu6zl/job_working_directory/000/20/outputs/dataset_0d3a43a5-d549-4889-af23-1bb4b48cd614.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 6: Color Deconvolution (toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/ip_color_deconvolution/0.9+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-16ed29cb9dad9eb6da055eb8f254c43cbad4eeb0:9c0a579c3a5099ce5691f17952f4725df3dcc592-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/0cbdf78fee14/color_deconvolution/color_deconvolution.py'  '/tmp/tmpvdrzu6zl/files/b/f/7/dataset_bf713c43-7324-497f-bccc-02ef5afd941d.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/24/outputs/dataset_efb8d821-4fbf-49e6-967d-c0498fedb44a.dat' 'rgb2hed'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tiff"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
convtype	`"rgb2hed"`
dbkey	`"?"`
isolate_channel	`None`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-16ed29cb9dad9eb6da055eb8f254c43cbad4eeb0:9c0a579c3a5099ce5691f17952f4725df3dcc592-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/0cbdf78fee14/color_deconvolution/color_deconvolution.py'  '/tmp/tmpvdrzu6zl/files/b/b/0/dataset_bb0bd6e3-1e9f-4b10-93b6-aa0312d1ae6c.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/21/outputs/dataset_8dffef90-1c9d-4b90-a4fa-dd41eda78929.dat' 'rgb2hed'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tiff"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
convtype	`"rgb2hed"`
dbkey	`"?"`
isolate_channel	`None`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-16ed29cb9dad9eb6da055eb8f254c43cbad4eeb0:9c0a579c3a5099ce5691f17952f4725df3dcc592-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/0cbdf78fee14/color_deconvolution/color_deconvolution.py'  '/tmp/tmpvdrzu6zl/files/a/7/f/dataset_a7f6f446-ac3a-4060-8f73-2a68b7a1a36e.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/22/outputs/dataset_c8fdbd14-7333-428d-ad47-7e1f0556bd3b.dat' 'rgb2hed'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tiff"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
convtype	`"rgb2hed"`
dbkey	`"?"`
isolate_channel	`None`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-16ed29cb9dad9eb6da055eb8f254c43cbad4eeb0:9c0a579c3a5099ce5691f17952f4725df3dcc592-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/0cbdf78fee14/color_deconvolution/color_deconvolution.py'  '/tmp/tmpvdrzu6zl/files/7/1/9/dataset_719cb02f-772c-446d-aca0-55166a0eaaf2.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/25/outputs/dataset_38f696de-b5df-44fd-97a9-e84cc9254dad.dat' 'rgb2hed'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tiff"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
convtype	`"rgb2hed"`
dbkey	`"?"`
isolate_channel	`None`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-16ed29cb9dad9eb6da055eb8f254c43cbad4eeb0:9c0a579c3a5099ce5691f17952f4725df3dcc592-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/0cbdf78fee14/color_deconvolution/color_deconvolution.py'  '/tmp/tmpvdrzu6zl/files/1/3/d/dataset_13d1aecd-badd-41d3-a146-864850a26d45.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/26/outputs/dataset_79da443f-2b4e-4cce-939c-7c53a26e48bb.dat' 'rgb2hed'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tiff"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
convtype	`"rgb2hed"`
dbkey	`"?"`
isolate_channel	`None`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-16ed29cb9dad9eb6da055eb8f254c43cbad4eeb0:9c0a579c3a5099ce5691f17952f4725df3dcc592-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/0cbdf78fee14/color_deconvolution/color_deconvolution.py'  '/tmp/tmpvdrzu6zl/files/e/c/6/dataset_ec6e2e14-ce7e-4f8c-b9bd-4d75c6336dd4.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/23/outputs/dataset_1fc77400-2dd4-47b6-9f96-78363c628647.dat' 'rgb2hed'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tiff"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
convtype	`"rgb2hed"`
dbkey	`"?"`
isolate_channel	`None`

Step 7: Width Extraction (Grep1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/4/4/d/dataset_44d763bc-cfa8-4a54-ba93-1b71ddbabdef.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/29/configs/tmp2tc82nv8'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/29/outputs/dataset_e82b2d9a-8434-4fe5-ad05-da3139ca58df.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Width ="`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/8/2/b/dataset_82bf864c-56e4-4fcd-ac0a-1c52e50c4a4f.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/30/configs/tmp04_cca6h'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/30/outputs/dataset_367bdd36-60eb-4803-8de9-4d3e0af76f22.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Width ="`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/3/a/b/dataset_3abcd0d8-a0cc-4e68-81ca-82971a0fbc94.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/27/configs/tmpl5vj1sdx'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/27/outputs/dataset_c7c80412-2e03-4b62-8cbf-7a13355bd830.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Width ="`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/0/d/3/dataset_0d3a43a5-d549-4889-af23-1bb4b48cd614.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/32/configs/tmp3xjwehr4'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/32/outputs/dataset_9d1de289-e546-4f3d-be1f-0d70e5450f86.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Width ="`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/a/2/7/dataset_a27ce60c-3cfa-4751-a175-fc6e301c8df6.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/28/configs/tmpziee_w4t'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/28/outputs/dataset_1f0f037f-82c4-4eab-998f-13fc1babc4e8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Width ="`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/c/b/f/dataset_cbf91b36-d00c-4e91-a2ad-7d3d87b179f6.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/31/configs/tmpb8zxzz25'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/31/outputs/dataset_ad66d355-e780-4171-a94d-f177498dfee9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Width ="`

Step 8: Height Extraction (Grep1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/3/a/b/dataset_3abcd0d8-a0cc-4e68-81ca-82971a0fbc94.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/33/configs/tmpurttt5tu'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/33/outputs/dataset_5805230e-7378-4c22-96a2-b8ce5fe82c4e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Height ="`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/a/2/7/dataset_a27ce60c-3cfa-4751-a175-fc6e301c8df6.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/34/configs/tmpwtzvzkqx'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/34/outputs/dataset_a430e356-ad6f-4e7d-847f-abde1a53028f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Height ="`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/8/2/b/dataset_82bf864c-56e4-4fcd-ac0a-1c52e50c4a4f.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/36/configs/tmpta40xl6w'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/36/outputs/dataset_666d4ee1-6f9d-4ec6-beed-b0be471f6842.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Height ="`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/4/4/d/dataset_44d763bc-cfa8-4a54-ba93-1b71ddbabdef.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/35/configs/tmpouoffgf6'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/35/outputs/dataset_19c068f8-b7c6-4c4a-bfd6-3808e2b2feb5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Height ="`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/c/b/f/dataset_cbf91b36-d00c-4e91-a2ad-7d3d87b179f6.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/37/configs/tmp7lc18bup'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/37/outputs/dataset_0c0a6cf7-b8fb-4d01-a880-7940e579c3e3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Height ="`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/tmp/tmpvdrzu6zl/files/0/d/3/dataset_0d3a43a5-d549-4889-af23-1bb4b48cd614.dat' | grep -P -f '/tmp/tmpvdrzu6zl/job_working_directory/000/38/configs/tmpd8upppdx'  >> '/tmp/tmpvdrzu6zl/job_working_directory/000/38/outputs/dataset_1c6a8a0d-3abf-4046-a19e-9a6c4652ccc4.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"Height ="`

Step 9: Split Image Channels for Staining Detection (toolshed.g2.bx.psu.edu/repos/imgteam/split_image/ip_split_image/2.3.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-4b113da51cc8adbc9a79baf6c7c613ff34cde372:2369eb9cdbeacf3d1cd55e745ea4f1ad598ddc59-0

Command Line:

mkdir output && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/split_image/390943df8a35/split_image/split.py'  '/tmp/tmpvdrzu6zl/files/e/f/b/dataset_efb8d821-4fbf-49e6-967d-c0498fedb44a.dat' 'C' output

Exit Code:

```
0
```

Standard Output:

Input image axes: YXC
Input image shape: (600, 600, 3)
Writing 3 image(s)
Output axes: YXC
Output shape: (600, 600, 1)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
axis	`"C"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
squeeze	`false`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-4b113da51cc8adbc9a79baf6c7c613ff34cde372:2369eb9cdbeacf3d1cd55e745ea4f1ad598ddc59-0

Command Line:

mkdir output && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/split_image/390943df8a35/split_image/split.py'  '/tmp/tmpvdrzu6zl/files/3/8/f/dataset_38f696de-b5df-44fd-97a9-e84cc9254dad.dat' 'C' output

Exit Code:

```
0
```

Standard Output:

Input image axes: YXC
Input image shape: (600, 600, 3)
Writing 3 image(s)
Output axes: YXC
Output shape: (600, 600, 1)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
axis	`"C"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
squeeze	`false`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-4b113da51cc8adbc9a79baf6c7c613ff34cde372:2369eb9cdbeacf3d1cd55e745ea4f1ad598ddc59-0

Command Line:

mkdir output && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/split_image/390943df8a35/split_image/split.py'  '/tmp/tmpvdrzu6zl/files/7/9/d/dataset_79da443f-2b4e-4cce-939c-7c53a26e48bb.dat' 'C' output

Exit Code:

```
0
```

Standard Output:

Input image axes: YXC
Input image shape: (600, 600, 3)
Writing 3 image(s)
Output axes: YXC
Output shape: (600, 600, 1)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
axis	`"C"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
squeeze	`false`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-4b113da51cc8adbc9a79baf6c7c613ff34cde372:2369eb9cdbeacf3d1cd55e745ea4f1ad598ddc59-0

Command Line:

mkdir output && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/split_image/390943df8a35/split_image/split.py'  '/tmp/tmpvdrzu6zl/files/8/d/f/dataset_8dffef90-1c9d-4b90-a4fa-dd41eda78929.dat' 'C' output

Exit Code:

```
0
```

Standard Output:

Input image axes: YXC
Input image shape: (600, 600, 3)
Writing 3 image(s)
Output axes: YXC
Output shape: (600, 600, 1)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
axis	`"C"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
squeeze	`false`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-4b113da51cc8adbc9a79baf6c7c613ff34cde372:2369eb9cdbeacf3d1cd55e745ea4f1ad598ddc59-0

Command Line:

mkdir output && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/split_image/390943df8a35/split_image/split.py'  '/tmp/tmpvdrzu6zl/files/c/8/f/dataset_c8fdbd14-7333-428d-ad47-7e1f0556bd3b.dat' 'C' output

Exit Code:

```
0
```

Standard Output:

Input image axes: YXC
Input image shape: (600, 600, 3)
Writing 3 image(s)
Output axes: YXC
Output shape: (600, 600, 1)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
axis	`"C"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
squeeze	`false`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-4b113da51cc8adbc9a79baf6c7c613ff34cde372:2369eb9cdbeacf3d1cd55e745ea4f1ad598ddc59-0

Command Line:

mkdir output && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/split_image/390943df8a35/split_image/split.py'  '/tmp/tmpvdrzu6zl/files/1/f/c/dataset_1fc77400-2dd4-47b6-9f96-78363c628647.dat' 'C' output

Exit Code:

```
0
```

Standard Output:

Input image axes: YXC
Input image shape: (600, 600, 3)
Writing 3 image(s)
Output axes: YXC
Output shape: (600, 600, 1)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
axis	`"C"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
squeeze	`false`

Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/49/configs/tmp6sctegj4' '/tmp/tmpvdrzu6zl/files/a/d/6/dataset_ad66d355-e780-4171-a94d-f177498dfee9.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/49/outputs/dataset_d4ca2786-c127-4cb9-82fd-e91a93b1c509.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 2:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/47/configs/tmps1_9sy_v' '/tmp/tmpvdrzu6zl/files/e/8/2/dataset_e82b2d9a-8434-4fe5-ad05-da3139ca58df.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/47/outputs/dataset_7b4a8a19-6c6d-4294-a561-5b7d0a60776e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 3:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/48/configs/tmpvage5sij' '/tmp/tmpvdrzu6zl/files/3/6/7/dataset_367bdd36-60eb-4803-8de9-4d3e0af76f22.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/48/outputs/dataset_09e0b70c-674d-46d2-ad79-0ed14faacffa.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 4:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/45/configs/tmpemepvx8q' '/tmp/tmpvdrzu6zl/files/c/7/c/dataset_c7c80412-2e03-4b62-8cbf-7a13355bd830.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/45/outputs/dataset_cfc873b5-e6ed-4d52-a45b-417b2b7d036c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 5:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/46/configs/tmpq14h842v' '/tmp/tmpvdrzu6zl/files/1/f/0/dataset_1f0f037f-82c4-4eab-998f-13fc1babc4e8.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/46/outputs/dataset_b86e7deb-828e-4449-9ceb-e1a514389938.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 6:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/50/configs/tmpjpvx9qpk' '/tmp/tmpvdrzu6zl/files/9/d/1/dataset_9d1de289-e546-4f3d-be1f-0d70e5450f86.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/50/outputs/dataset_678bf0ec-ee4c-4e30-b84c-63ce9824f6f5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/53/configs/tmp4ntifb1i' '/tmp/tmpvdrzu6zl/files/1/9/c/dataset_19c068f8-b7c6-4c4a-bfd6-3808e2b2feb5.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/53/outputs/dataset_cbcf4542-1f04-456d-9a77-32072b1f86cb.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 2:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/56/configs/tmp4uue097f' '/tmp/tmpvdrzu6zl/files/1/c/6/dataset_1c6a8a0d-3abf-4046-a19e-9a6c4652ccc4.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/56/outputs/dataset_72fdd91b-510c-40f2-a9d2-7366fbb2c40b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 3:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/51/configs/tmp0a6cf2zh' '/tmp/tmpvdrzu6zl/files/5/8/0/dataset_5805230e-7378-4c22-96a2-b8ce5fe82c4e.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/51/outputs/dataset_cc0ec2dc-6de3-42a2-a397-d7a4ac637848.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 4:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/52/configs/tmp2yi8a597' '/tmp/tmpvdrzu6zl/files/a/4/3/dataset_a430e356-ad6f-4e7d-847f-abde1a53028f.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/52/outputs/dataset_e7ef501c-4f6f-4501-9d84-f3bd351c82ac.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 5:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/54/configs/tmpfdv9frmq' '/tmp/tmpvdrzu6zl/files/6/6/6/dataset_666d4ee1-6f9d-4ec6-beed-b0be471f6842.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/54/outputs/dataset_52216c76-af62-4641-81ea-61028db3a3a4.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Job 6:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmpvdrzu6zl/job_working_directory/000/55/configs/tmpxr_nhb34' '/tmp/tmpvdrzu6zl/files/0/c/0/dataset_0c0a6cf7-b8fb-4d01-a880-7940e579c3e3.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/55/outputs/dataset_de6b44cc-df71-4f18-a8a1-7c3080e67480.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/.*= //"`
dbkey	`"?"`

Step 12: Collection: Extract Stain Channel from Sub-Collections (__EXTRACT_DATASET__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
input	`{"values": [{"id": 37, "src": "dce"}]}`
which	`{"__current_case__": 2, "index": "1", "which_dataset": "by_index"}`

Job 2:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
input	`{"values": [{"id": 38, "src": "dce"}]}`
which	`{"__current_case__": 2, "index": "1", "which_dataset": "by_index"}`

Job 3:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
input	`{"values": [{"id": 39, "src": "dce"}]}`
which	`{"__current_case__": 2, "index": "1", "which_dataset": "by_index"}`

Job 4:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
input	`{"values": [{"id": 40, "src": "dce"}]}`
which	`{"__current_case__": 2, "index": "1", "which_dataset": "by_index"}`

Job 5:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
input	`{"values": [{"id": 41, "src": "dce"}]}`
which	`{"__current_case__": 2, "index": "1", "which_dataset": "by_index"}`

Job 6:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
input	`{"values": [{"id": 42, "src": "dce"}]}`
which	`{"__current_case__": 2, "index": "1", "which_dataset": "by_index"}`

Step 13: Unlabelled step (Paste1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/c/f/c/dataset_cfc873b5-e6ed-4d52-a45b-417b2b7d036c.dat' '/tmp/tmpvdrzu6zl/files/c/c/0/dataset_cc0ec2dc-6de3-42a2-a397-d7a4ac637848.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/57/outputs/dataset_16f1a1ba-7dbf-48d7-9bbf-361914192834.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/0/9/e/dataset_09e0b70c-674d-46d2-ad79-0ed14faacffa.dat' '/tmp/tmpvdrzu6zl/files/5/2/2/dataset_52216c76-af62-4641-81ea-61028db3a3a4.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/60/outputs/dataset_6837b39c-5d24-4651-bea4-846b014a6461.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/d/4/c/dataset_d4ca2786-c127-4cb9-82fd-e91a93b1c509.dat' '/tmp/tmpvdrzu6zl/files/d/e/6/dataset_de6b44cc-df71-4f18-a8a1-7c3080e67480.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/61/outputs/dataset_71ce2bfd-3f0b-47ec-bcd2-d76378a30b9f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/b/8/6/dataset_b86e7deb-828e-4449-9ceb-e1a514389938.dat' '/tmp/tmpvdrzu6zl/files/e/7/e/dataset_e7ef501c-4f6f-4501-9d84-f3bd351c82ac.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/58/outputs/dataset_e458dd38-fb42-4970-acf9-ce0f95b41a2b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/7/b/4/dataset_7b4a8a19-6c6d-4294-a561-5b7d0a60776e.dat' '/tmp/tmpvdrzu6zl/files/c/b/c/dataset_cbcf4542-1f04-456d-9a77-32072b1f86cb.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/59/outputs/dataset_ecca6edf-d164-4ed6-bce8-34f48c855ad3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/6/7/8/dataset_678bf0ec-ee4c-4e30-b84c-63ce9824f6f5.dat' '/tmp/tmpvdrzu6zl/files/7/2/f/dataset_72fdd91b-510c-40f2-a9d2-7366fbb2c40b.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/62/outputs/dataset_eecbbe79-9189-4af3-8836-53f46b289e6c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Step 14: Threshold Stain Channel Collection (toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.25.2+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-73e393604573445b115df8bb46e40eaa3d54b806:33baf870bedadfd56454e642b719ac19184cb7ed-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/2ee04d2ebdcf/2d_auto_threshold/auto_threshold.py'  --input '/tmp/tmpvdrzu6zl/files/5/1/3/dataset_51388505-430a-4215-94e8-8556e5770219.dat'  --output ./out.tiff --params '/tmp/tmpvdrzu6zl/job_working_directory/000/83/configs/tmpl8z0nbsj' --verbose

Exit Code:

```
0
```

Standard Output:

[input] Input image axes: YXC
[input] Input image shape: (600, 600, 1)
[input] Input image dtype: float32
[input] Input image resolution=(1.0, 1.0), unit='inch'
Thresholding: threshold_otsu with offset=0.0, invert=False
[output] Output image axes: YXC
[output] Output image shape: (600, 600, 1)
[output] Output image dtype: uint8
[output] Output image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert_output	`false`
th_method	`{"__current_case__": 1, "method_id": "otsu", "offset": "0.0"}`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-73e393604573445b115df8bb46e40eaa3d54b806:33baf870bedadfd56454e642b719ac19184cb7ed-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/2ee04d2ebdcf/2d_auto_threshold/auto_threshold.py'  --input '/tmp/tmpvdrzu6zl/files/f/7/c/dataset_f7c0c296-f430-49f7-a474-91586395aa96.dat'  --output ./out.tiff --params '/tmp/tmpvdrzu6zl/job_working_directory/000/84/configs/tmpzksmcefy' --verbose

Exit Code:

```
0
```

Standard Output:

[input] Input image axes: YXC
[input] Input image shape: (600, 600, 1)
[input] Input image dtype: float32
[input] Input image resolution=(1.0, 1.0), unit='inch'
Thresholding: threshold_otsu with offset=0.0, invert=False
[output] Output image axes: YXC
[output] Output image shape: (600, 600, 1)
[output] Output image dtype: uint8
[output] Output image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert_output	`false`
th_method	`{"__current_case__": 1, "method_id": "otsu", "offset": "0.0"}`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-73e393604573445b115df8bb46e40eaa3d54b806:33baf870bedadfd56454e642b719ac19184cb7ed-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/2ee04d2ebdcf/2d_auto_threshold/auto_threshold.py'  --input '/tmp/tmpvdrzu6zl/files/5/5/e/dataset_55ec72ac-c0b5-4744-b6fc-0694cc2dd780.dat'  --output ./out.tiff --params '/tmp/tmpvdrzu6zl/job_working_directory/000/85/configs/tmp0gjn6b43' --verbose

Exit Code:

```
0
```

Standard Output:

[input] Input image axes: YXC
[input] Input image shape: (600, 600, 1)
[input] Input image dtype: float32
[input] Input image resolution=(1.0, 1.0), unit='inch'
Thresholding: threshold_otsu with offset=0.0, invert=False
[output] Output image axes: YXC
[output] Output image shape: (600, 600, 1)
[output] Output image dtype: uint8
[output] Output image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert_output	`false`
th_method	`{"__current_case__": 1, "method_id": "otsu", "offset": "0.0"}`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-73e393604573445b115df8bb46e40eaa3d54b806:33baf870bedadfd56454e642b719ac19184cb7ed-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/2ee04d2ebdcf/2d_auto_threshold/auto_threshold.py'  --input '/tmp/tmpvdrzu6zl/files/a/b/c/dataset_abcb6b34-33d5-4f9e-81fd-168dde47a31d.dat'  --output ./out.tiff --params '/tmp/tmpvdrzu6zl/job_working_directory/000/86/configs/tmpjrvyyuq_' --verbose

Exit Code:

```
0
```

Standard Output:

[input] Input image axes: YXC
[input] Input image shape: (600, 600, 1)
[input] Input image dtype: float32
[input] Input image resolution=(1.0, 1.0), unit='inch'
Thresholding: threshold_otsu with offset=0.0, invert=False
[output] Output image axes: YXC
[output] Output image shape: (600, 600, 1)
[output] Output image dtype: uint8
[output] Output image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert_output	`false`
th_method	`{"__current_case__": 1, "method_id": "otsu", "offset": "0.0"}`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-73e393604573445b115df8bb46e40eaa3d54b806:33baf870bedadfd56454e642b719ac19184cb7ed-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/2ee04d2ebdcf/2d_auto_threshold/auto_threshold.py'  --input '/tmp/tmpvdrzu6zl/files/b/4/a/dataset_b4a6f92c-ce0c-4aef-89b0-4f5156f9802e.dat'  --output ./out.tiff --params '/tmp/tmpvdrzu6zl/job_working_directory/000/87/configs/tmpfpf8j4sr' --verbose

Exit Code:

```
0
```

Standard Output:

[input] Input image axes: YXC
[input] Input image shape: (600, 600, 1)
[input] Input image dtype: float32
[input] Input image resolution=(1.0, 1.0), unit='inch'
Thresholding: threshold_otsu with offset=0.0, invert=False
[output] Output image axes: YXC
[output] Output image shape: (600, 600, 1)
[output] Output image dtype: uint8
[output] Output image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert_output	`false`
th_method	`{"__current_case__": 1, "method_id": "otsu", "offset": "0.0"}`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-73e393604573445b115df8bb46e40eaa3d54b806:33baf870bedadfd56454e642b719ac19184cb7ed-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/2ee04d2ebdcf/2d_auto_threshold/auto_threshold.py'  --input '/tmp/tmpvdrzu6zl/files/0/e/a/dataset_0eacba73-8a4e-481d-bf23-49051ec8fe7a.dat'  --output ./out.tiff --params '/tmp/tmpvdrzu6zl/job_working_directory/000/88/configs/tmpfhdhrtqs' --verbose

Exit Code:

```
0
```

Standard Output:

[input] Input image axes: YXC
[input] Input image shape: (600, 600, 1)
[input] Input image dtype: float32
[input] Input image resolution=(1.0, 1.0), unit='inch'
Thresholding: threshold_otsu with offset=0.0, invert=False
[output] Output image axes: YXC
[output] Output image shape: (600, 600, 1)
[output] Output image dtype: uint8
[output] Output image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert_output	`false`
th_method	`{"__current_case__": 1, "method_id": "otsu", "offset": "0.0"}`

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/61f9ddbc63ca/column_maker/column_maker.py' --column-types int,int  --file '/tmp/tmpvdrzu6zl/job_working_directory/000/64/configs/tmpdo24yn7g' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpvdrzu6zl/files/e/4/5/dataset_e458dd38-fb42-4970-acf9-ce0f95b41a2b.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/64/outputs/dataset_482545ad-7a6e-4d49-84ff-a6a453d6159c.dat'

Exit Code:

```
0
```

Standard Output:

c1 * c2
Computing 1 new columns with instructions ['c1 * c2;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c1 * c2"}], "header_lines_select": "no"}`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/61f9ddbc63ca/column_maker/column_maker.py' --column-types int,int  --file '/tmp/tmpvdrzu6zl/job_working_directory/000/63/configs/tmpm2l4apkv' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpvdrzu6zl/files/1/6/f/dataset_16f1a1ba-7dbf-48d7-9bbf-361914192834.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/63/outputs/dataset_bf96a9c3-37bd-43a4-9d78-5137dffd8e72.dat'

Exit Code:

```
0
```

Standard Output:

c1 * c2
Computing 1 new columns with instructions ['c1 * c2;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c1 * c2"}], "header_lines_select": "no"}`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/61f9ddbc63ca/column_maker/column_maker.py' --column-types int,int  --file '/tmp/tmpvdrzu6zl/job_working_directory/000/65/configs/tmp9iv4psfx' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpvdrzu6zl/files/e/c/c/dataset_ecca6edf-d164-4ed6-bce8-34f48c855ad3.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/65/outputs/dataset_7b8c38b0-1ab2-4b26-a7a2-eee02f3526c4.dat'

Exit Code:

```
0
```

Standard Output:

c1 * c2
Computing 1 new columns with instructions ['c1 * c2;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c1 * c2"}], "header_lines_select": "no"}`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/61f9ddbc63ca/column_maker/column_maker.py' --column-types int,int  --file '/tmp/tmpvdrzu6zl/job_working_directory/000/66/configs/tmppj9vogsh' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpvdrzu6zl/files/6/8/3/dataset_6837b39c-5d24-4651-bea4-846b014a6461.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/66/outputs/dataset_e46167a8-dc50-4838-b6d1-28b1c1ba87f4.dat'

Exit Code:

```
0
```

Standard Output:

c1 * c2
Computing 1 new columns with instructions ['c1 * c2;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c1 * c2"}], "header_lines_select": "no"}`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/61f9ddbc63ca/column_maker/column_maker.py' --column-types int,int  --file '/tmp/tmpvdrzu6zl/job_working_directory/000/67/configs/tmp8_8cqx3p' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpvdrzu6zl/files/7/1/c/dataset_71ce2bfd-3f0b-47ec-bcd2-d76378a30b9f.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/67/outputs/dataset_5d0a1343-9718-43e8-9c66-c8b550abdcce.dat'

Exit Code:

```
0
```

Standard Output:

c1 * c2
Computing 1 new columns with instructions ['c1 * c2;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c1 * c2"}], "header_lines_select": "no"}`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/61f9ddbc63ca/column_maker/column_maker.py' --column-types int,int  --file '/tmp/tmpvdrzu6zl/job_working_directory/000/68/configs/tmp54fsjrsk' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpvdrzu6zl/files/e/e/c/dataset_eecbbe79-9189-4af3-8836-53f46b289e6c.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/68/outputs/dataset_e136129c-e270-498a-a8ff-268db5864005.dat'

Exit Code:

```
0
```

Standard Output:

c1 * c2
Computing 1 new columns with instructions ['c1 * c2;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c1 * c2"}], "header_lines_select": "no"}`

Step 16: Generate ROIs of stained region (toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary/20240614+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-557813cb01abcc9c2a8cf25415af954884af9f02:a09946e2cdd9514dc626a55ca61fbbd9c05f6fe2-0

Command Line:

ln -s '/tmp/tmpvdrzu6zl/files/9/c/0/dataset_9c002208-8892-43a0-8fb8-5776a9c6a482.dat' './dataset_9c002208-8892-43a0-8fb8-5776a9c6a482.tiff' && touch 'output.tiff' && ImageJ --ij2 --headless --debug --jython '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py' '/tmp/tmpvdrzu6zl/job_working_directory/000/89/outputs/dataset_4ba2c9ab-4446-468b-82e4-55d66949da3d.dat' '/tmp/tmpvdrzu6zl/files/9/c/0/dataset_9c002208-8892-43a0-8fb8-5776a9c6a482.dat' 'yes' '2-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'output.tiff' 'tiff' '' && mv 'output.tiff' '/tmp/tmpvdrzu6zl/job_working_directory/000/89/outputs/dataset_006f8ffc-f9f6-48af-b0f8-6b64439c551c.dat';

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/ImageJ: line 8: /usr/local/bin/../share/ImageJ.cfg: Permission denied
Available RAM: 12145MB, using 3/4 of that: 9109MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Re-executing with correct library lookup path (/usr/local/share/lib/linux64:/usr/local/share/mm/linux64)
Available RAM: 12145MB, using 3/4 of that: 9109MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Using JAVA_HOME /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre
Opening Java library /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre/lib/amd64/server/libjvm.so
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Adding option: -Djava.home=/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64/
ij1.plugin.dirs: null
$HOME/.plugins: ?/.plugins does not exist
Launching main class org.python.util.jython with parameters [/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py, /tmp/tmpvdrzu6zl/job_working_directory/000/89/outputs/dataset_4ba2c9ab-4446-468b-82e4-55d66949da3d.dat, /tmp/tmpvdrzu6zl/files/9/c/0/dataset_9c002208-8892-43a0-8fb8-5776a9c6a482.dat, yes, 2-Infinity, 0.0, 1.0, Outlines, no, no, no, output.tiff, tiff, ]
Class loader = sun.misc.Launcher$AppClassLoader@764c12b6

Standard Output:

java -Dpython.cachedir.skip=true -Dplugins.dir=/usr/local/share -Xmx9109m -Djava.awt.headless=true -Dapple.awt.UIElement=true -Xincgc -XX:PermSize=128m -Djava.class.path=/usr/local/share/jars/imagej-launcher-6.0.2.jar -Dimagej.dir=/usr/local/share -Dij.dir=/usr/local/share -Dfiji.dir=/usr/local/share -Dfiji.defaultLibPath=lib/amd64/server/libjvm.so -Dfiji.executable=ImageJ_bin -Dij.executable=ImageJ_bin -Djava.library.path=/usr/local/share/lib/linux64:/usr/local/share/mm/linux64 -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath /usr/share/java/jython.jar -classpath . -ijjarpath jars -ijjarpath plugins org.python.util.jython /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py /tmp/tmpvdrzu6zl/job_working_directory/000/89/outputs/dataset_4ba2c9ab-4446-468b-82e4-55d66949da3d.dat /tmp/tmpvdrzu6zl/files/9/c/0/dataset_9c002208-8892-43a0-8fb8-5776a9c6a482.dat yes 2-Infinity 0.0 1.0 Outlines no no no output.tiff tiff

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
black_background	`"yes"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
circularity_max	`"1.0"`
circularity_min	`"0.0"`
dbkey	`"?"`
display_results	`"no"`
exclude_edges	`"no"`
export_rois	`true`
include_holes	`"no"`
show	`"Outlines"`
size	`"2-Infinity"`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-557813cb01abcc9c2a8cf25415af954884af9f02:a09946e2cdd9514dc626a55ca61fbbd9c05f6fe2-0

Command Line:

ln -s '/tmp/tmpvdrzu6zl/files/f/f/4/dataset_ff458793-1654-43da-8306-26105e8ff5d2.dat' './dataset_ff458793-1654-43da-8306-26105e8ff5d2.tiff' && touch 'output.tiff' && ImageJ --ij2 --headless --debug --jython '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py' '/tmp/tmpvdrzu6zl/job_working_directory/000/90/outputs/dataset_198d90ad-8f5b-491b-b40a-58b5337cc8d4.dat' '/tmp/tmpvdrzu6zl/files/f/f/4/dataset_ff458793-1654-43da-8306-26105e8ff5d2.dat' 'yes' '2-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'output.tiff' 'tiff' '' && mv 'output.tiff' '/tmp/tmpvdrzu6zl/job_working_directory/000/90/outputs/dataset_53d2651a-5f52-46e2-b6f0-aa784598c3fb.dat';

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/ImageJ: line 8: /usr/local/bin/../share/ImageJ.cfg: Permission denied
Available RAM: 12156MB, using 3/4 of that: 9117MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Re-executing with correct library lookup path (/usr/local/share/lib/linux64:/usr/local/share/mm/linux64)
Available RAM: 12156MB, using 3/4 of that: 9117MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Using JAVA_HOME /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre
Opening Java library /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre/lib/amd64/server/libjvm.so
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Adding option: -Djava.home=/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64/
ij1.plugin.dirs: null
$HOME/.plugins: ?/.plugins does not exist
Launching main class org.python.util.jython with parameters [/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py, /tmp/tmpvdrzu6zl/job_working_directory/000/90/outputs/dataset_198d90ad-8f5b-491b-b40a-58b5337cc8d4.dat, /tmp/tmpvdrzu6zl/files/f/f/4/dataset_ff458793-1654-43da-8306-26105e8ff5d2.dat, yes, 2-Infinity, 0.0, 1.0, Outlines, no, no, no, output.tiff, tiff, ]
Class loader = sun.misc.Launcher$AppClassLoader@764c12b6

Standard Output:

java -Dpython.cachedir.skip=true -Dplugins.dir=/usr/local/share -Xmx9117m -Djava.awt.headless=true -Dapple.awt.UIElement=true -Xincgc -XX:PermSize=128m -Djava.class.path=/usr/local/share/jars/imagej-launcher-6.0.2.jar -Dimagej.dir=/usr/local/share -Dij.dir=/usr/local/share -Dfiji.dir=/usr/local/share -Dfiji.defaultLibPath=lib/amd64/server/libjvm.so -Dfiji.executable=ImageJ_bin -Dij.executable=ImageJ_bin -Djava.library.path=/usr/local/share/lib/linux64:/usr/local/share/mm/linux64 -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath /usr/share/java/jython.jar -classpath . -ijjarpath jars -ijjarpath plugins org.python.util.jython /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py /tmp/tmpvdrzu6zl/job_working_directory/000/90/outputs/dataset_198d90ad-8f5b-491b-b40a-58b5337cc8d4.dat /tmp/tmpvdrzu6zl/files/f/f/4/dataset_ff458793-1654-43da-8306-26105e8ff5d2.dat yes 2-Infinity 0.0 1.0 Outlines no no no output.tiff tiff

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
black_background	`"yes"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
circularity_max	`"1.0"`
circularity_min	`"0.0"`
dbkey	`"?"`
display_results	`"no"`
exclude_edges	`"no"`
export_rois	`true`
include_holes	`"no"`
show	`"Outlines"`
size	`"2-Infinity"`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-557813cb01abcc9c2a8cf25415af954884af9f02:a09946e2cdd9514dc626a55ca61fbbd9c05f6fe2-0

Command Line:

ln -s '/tmp/tmpvdrzu6zl/files/6/1/4/dataset_6142c827-f4b0-4850-81c8-0ddec9a98f4c.dat' './dataset_6142c827-f4b0-4850-81c8-0ddec9a98f4c.tiff' && touch 'output.tiff' && ImageJ --ij2 --headless --debug --jython '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py' '/tmp/tmpvdrzu6zl/job_working_directory/000/91/outputs/dataset_8717757a-d577-43a3-aa3f-95a0279ae450.dat' '/tmp/tmpvdrzu6zl/files/6/1/4/dataset_6142c827-f4b0-4850-81c8-0ddec9a98f4c.dat' 'yes' '2-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'output.tiff' 'tiff' '' && mv 'output.tiff' '/tmp/tmpvdrzu6zl/job_working_directory/000/91/outputs/dataset_91cbbf50-909b-439d-af05-550b2f3980c3.dat';

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/ImageJ: line 8: /usr/local/bin/../share/ImageJ.cfg: Permission denied
Available RAM: 12109MB, using 3/4 of that: 9082MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Re-executing with correct library lookup path (/usr/local/share/lib/linux64:/usr/local/share/mm/linux64)
Available RAM: 12109MB, using 3/4 of that: 9082MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Using JAVA_HOME /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre
Opening Java library /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre/lib/amd64/server/libjvm.so
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Adding option: -Djava.home=/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64/
ij1.plugin.dirs: null
$HOME/.plugins: ?/.plugins does not exist
Launching main class org.python.util.jython with parameters [/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py, /tmp/tmpvdrzu6zl/job_working_directory/000/91/outputs/dataset_8717757a-d577-43a3-aa3f-95a0279ae450.dat, /tmp/tmpvdrzu6zl/files/6/1/4/dataset_6142c827-f4b0-4850-81c8-0ddec9a98f4c.dat, yes, 2-Infinity, 0.0, 1.0, Outlines, no, no, no, output.tiff, tiff, ]
Class loader = sun.misc.Launcher$AppClassLoader@764c12b6

Standard Output:

java -Dpython.cachedir.skip=true -Dplugins.dir=/usr/local/share -Xmx9082m -Djava.awt.headless=true -Dapple.awt.UIElement=true -Xincgc -XX:PermSize=128m -Djava.class.path=/usr/local/share/jars/imagej-launcher-6.0.2.jar -Dimagej.dir=/usr/local/share -Dij.dir=/usr/local/share -Dfiji.dir=/usr/local/share -Dfiji.defaultLibPath=lib/amd64/server/libjvm.so -Dfiji.executable=ImageJ_bin -Dij.executable=ImageJ_bin -Djava.library.path=/usr/local/share/lib/linux64:/usr/local/share/mm/linux64 -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath /usr/share/java/jython.jar -classpath . -ijjarpath jars -ijjarpath plugins org.python.util.jython /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py /tmp/tmpvdrzu6zl/job_working_directory/000/91/outputs/dataset_8717757a-d577-43a3-aa3f-95a0279ae450.dat /tmp/tmpvdrzu6zl/files/6/1/4/dataset_6142c827-f4b0-4850-81c8-0ddec9a98f4c.dat yes 2-Infinity 0.0 1.0 Outlines no no no output.tiff tiff

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
black_background	`"yes"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
circularity_max	`"1.0"`
circularity_min	`"0.0"`
dbkey	`"?"`
display_results	`"no"`
exclude_edges	`"no"`
export_rois	`true`
include_holes	`"no"`
show	`"Outlines"`
size	`"2-Infinity"`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-557813cb01abcc9c2a8cf25415af954884af9f02:a09946e2cdd9514dc626a55ca61fbbd9c05f6fe2-0

Command Line:

ln -s '/tmp/tmpvdrzu6zl/files/c/c/c/dataset_cccaad4c-4208-43f3-a991-be5189021f60.dat' './dataset_cccaad4c-4208-43f3-a991-be5189021f60.tiff' && touch 'output.tiff' && ImageJ --ij2 --headless --debug --jython '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py' '/tmp/tmpvdrzu6zl/job_working_directory/000/92/outputs/dataset_ac431dbd-2757-4ed1-a7dc-c71759865ece.dat' '/tmp/tmpvdrzu6zl/files/c/c/c/dataset_cccaad4c-4208-43f3-a991-be5189021f60.dat' 'yes' '2-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'output.tiff' 'tiff' '' && mv 'output.tiff' '/tmp/tmpvdrzu6zl/job_working_directory/000/92/outputs/dataset_3d4f0499-0e9d-4b72-b95f-226b9b4ad1a6.dat';

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/ImageJ: line 8: /usr/local/bin/../share/ImageJ.cfg: Permission denied
Available RAM: 12122MB, using 3/4 of that: 9092MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Re-executing with correct library lookup path (/usr/local/share/lib/linux64:/usr/local/share/mm/linux64)
Available RAM: 12122MB, using 3/4 of that: 9092MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Using JAVA_HOME /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre
Opening Java library /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre/lib/amd64/server/libjvm.so
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Adding option: -Djava.home=/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64/
ij1.plugin.dirs: null
$HOME/.plugins: ?/.plugins does not exist
Launching main class org.python.util.jython with parameters [/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py, /tmp/tmpvdrzu6zl/job_working_directory/000/92/outputs/dataset_ac431dbd-2757-4ed1-a7dc-c71759865ece.dat, /tmp/tmpvdrzu6zl/files/c/c/c/dataset_cccaad4c-4208-43f3-a991-be5189021f60.dat, yes, 2-Infinity, 0.0, 1.0, Outlines, no, no, no, output.tiff, tiff, ]
Class loader = sun.misc.Launcher$AppClassLoader@764c12b6

Standard Output:

java -Dpython.cachedir.skip=true -Dplugins.dir=/usr/local/share -Xmx9092m -Djava.awt.headless=true -Dapple.awt.UIElement=true -Xincgc -XX:PermSize=128m -Djava.class.path=/usr/local/share/jars/imagej-launcher-6.0.2.jar -Dimagej.dir=/usr/local/share -Dij.dir=/usr/local/share -Dfiji.dir=/usr/local/share -Dfiji.defaultLibPath=lib/amd64/server/libjvm.so -Dfiji.executable=ImageJ_bin -Dij.executable=ImageJ_bin -Djava.library.path=/usr/local/share/lib/linux64:/usr/local/share/mm/linux64 -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath /usr/share/java/jython.jar -classpath . -ijjarpath jars -ijjarpath plugins org.python.util.jython /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py /tmp/tmpvdrzu6zl/job_working_directory/000/92/outputs/dataset_ac431dbd-2757-4ed1-a7dc-c71759865ece.dat /tmp/tmpvdrzu6zl/files/c/c/c/dataset_cccaad4c-4208-43f3-a991-be5189021f60.dat yes 2-Infinity 0.0 1.0 Outlines no no no output.tiff tiff

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
black_background	`"yes"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
circularity_max	`"1.0"`
circularity_min	`"0.0"`
dbkey	`"?"`
display_results	`"no"`
exclude_edges	`"no"`
export_rois	`true`
include_holes	`"no"`
show	`"Outlines"`
size	`"2-Infinity"`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-557813cb01abcc9c2a8cf25415af954884af9f02:a09946e2cdd9514dc626a55ca61fbbd9c05f6fe2-0

Command Line:

ln -s '/tmp/tmpvdrzu6zl/files/a/c/4/dataset_ac4511e3-0c91-4ad6-9397-b74b8c5510e9.dat' './dataset_ac4511e3-0c91-4ad6-9397-b74b8c5510e9.tiff' && touch 'output.tiff' && ImageJ --ij2 --headless --debug --jython '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py' '/tmp/tmpvdrzu6zl/job_working_directory/000/93/outputs/dataset_7e23b31d-dcd5-4d13-986d-7144d8efb7cc.dat' '/tmp/tmpvdrzu6zl/files/a/c/4/dataset_ac4511e3-0c91-4ad6-9397-b74b8c5510e9.dat' 'yes' '2-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'output.tiff' 'tiff' '' && mv 'output.tiff' '/tmp/tmpvdrzu6zl/job_working_directory/000/93/outputs/dataset_ea87ac7e-1767-45ab-983d-22f697db7d21.dat';

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/ImageJ: line 8: /usr/local/bin/../share/ImageJ.cfg: Permission denied
Available RAM: 12132MB, using 3/4 of that: 9099MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Re-executing with correct library lookup path (/usr/local/share/lib/linux64:/usr/local/share/mm/linux64)
Available RAM: 12132MB, using 3/4 of that: 9099MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Using JAVA_HOME /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre
Opening Java library /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre/lib/amd64/server/libjvm.so
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Adding option: -Djava.home=/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64/
ij1.plugin.dirs: null
$HOME/.plugins: ?/.plugins does not exist
Launching main class org.python.util.jython with parameters [/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py, /tmp/tmpvdrzu6zl/job_working_directory/000/93/outputs/dataset_7e23b31d-dcd5-4d13-986d-7144d8efb7cc.dat, /tmp/tmpvdrzu6zl/files/a/c/4/dataset_ac4511e3-0c91-4ad6-9397-b74b8c5510e9.dat, yes, 2-Infinity, 0.0, 1.0, Outlines, no, no, no, output.tiff, tiff, ]
Class loader = sun.misc.Launcher$AppClassLoader@764c12b6

Standard Output:

java -Dpython.cachedir.skip=true -Dplugins.dir=/usr/local/share -Xmx9099m -Djava.awt.headless=true -Dapple.awt.UIElement=true -Xincgc -XX:PermSize=128m -Djava.class.path=/usr/local/share/jars/imagej-launcher-6.0.2.jar -Dimagej.dir=/usr/local/share -Dij.dir=/usr/local/share -Dfiji.dir=/usr/local/share -Dfiji.defaultLibPath=lib/amd64/server/libjvm.so -Dfiji.executable=ImageJ_bin -Dij.executable=ImageJ_bin -Djava.library.path=/usr/local/share/lib/linux64:/usr/local/share/mm/linux64 -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath /usr/share/java/jython.jar -classpath . -ijjarpath jars -ijjarpath plugins org.python.util.jython /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py /tmp/tmpvdrzu6zl/job_working_directory/000/93/outputs/dataset_7e23b31d-dcd5-4d13-986d-7144d8efb7cc.dat /tmp/tmpvdrzu6zl/files/a/c/4/dataset_ac4511e3-0c91-4ad6-9397-b74b8c5510e9.dat yes 2-Infinity 0.0 1.0 Outlines no no no output.tiff tiff

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
black_background	`"yes"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
circularity_max	`"1.0"`
circularity_min	`"0.0"`
dbkey	`"?"`
display_results	`"no"`
exclude_edges	`"no"`
export_rois	`true`
include_holes	`"no"`
show	`"Outlines"`
size	`"2-Infinity"`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-557813cb01abcc9c2a8cf25415af954884af9f02:a09946e2cdd9514dc626a55ca61fbbd9c05f6fe2-0

Command Line:

ln -s '/tmp/tmpvdrzu6zl/files/d/9/4/dataset_d94dad0b-8c76-4d12-994b-cd54f49df863.dat' './dataset_d94dad0b-8c76-4d12-994b-cd54f49df863.tiff' && touch 'output.tiff' && ImageJ --ij2 --headless --debug --jython '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py' '/tmp/tmpvdrzu6zl/job_working_directory/000/94/outputs/dataset_5de7e016-1b75-410c-a8b0-954f76b7c866.dat' '/tmp/tmpvdrzu6zl/files/d/9/4/dataset_d94dad0b-8c76-4d12-994b-cd54f49df863.dat' 'yes' '2-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'output.tiff' 'tiff' '' && mv 'output.tiff' '/tmp/tmpvdrzu6zl/job_working_directory/000/94/outputs/dataset_10d36b86-47a7-4fc2-a4f9-f6cf35b6f0c4.dat';

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/ImageJ: line 8: /usr/local/bin/../share/ImageJ.cfg: Permission denied
Available RAM: 12132MB, using 3/4 of that: 9099MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Re-executing with correct library lookup path (/usr/local/share/lib/linux64:/usr/local/share/mm/linux64)
Available RAM: 12132MB, using 3/4 of that: 9099MB
JRE not found in '/usr/local/share/jre'
JAVA_HOME contains a JRE: '/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre'
Using JAVA_HOME /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre
Opening Java library /usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64//jre/lib/amd64/server/libjvm.so
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Adding option: -Djava.home=/usr/local/share/java/linux-amd64/zulu8.60.0.21-ca-fx-jdk8.0.322-linux_x64/
ij1.plugin.dirs: null
$HOME/.plugins: ?/.plugins does not exist
Launching main class org.python.util.jython with parameters [/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py, /tmp/tmpvdrzu6zl/job_working_directory/000/94/outputs/dataset_5de7e016-1b75-410c-a8b0-954f76b7c866.dat, /tmp/tmpvdrzu6zl/files/d/9/4/dataset_d94dad0b-8c76-4d12-994b-cd54f49df863.dat, yes, 2-Infinity, 0.0, 1.0, Outlines, no, no, no, output.tiff, tiff, ]
Class loader = sun.misc.Launcher$AppClassLoader@764c12b6

Standard Output:

java -Dpython.cachedir.skip=true -Dplugins.dir=/usr/local/share -Xmx9099m -Djava.awt.headless=true -Dapple.awt.UIElement=true -Xincgc -XX:PermSize=128m -Djava.class.path=/usr/local/share/jars/imagej-launcher-6.0.2.jar -Dimagej.dir=/usr/local/share -Dij.dir=/usr/local/share -Dfiji.dir=/usr/local/share -Dfiji.defaultLibPath=lib/amd64/server/libjvm.so -Dfiji.executable=ImageJ_bin -Dij.executable=ImageJ_bin -Djava.library.path=/usr/local/share/lib/linux64:/usr/local/share/mm/linux64 -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath /usr/share/java/jython.jar -classpath . -ijjarpath jars -ijjarpath plugins org.python.util.jython /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/862af85a50ec/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary_jython_script.py /tmp/tmpvdrzu6zl/job_working_directory/000/94/outputs/dataset_5de7e016-1b75-410c-a8b0-954f76b7c866.dat /tmp/tmpvdrzu6zl/files/d/9/4/dataset_d94dad0b-8c76-4d12-994b-cd54f49df863.dat yes 2-Infinity 0.0 1.0 Outlines no no no output.tiff tiff

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
black_background	`"yes"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
circularity_max	`"1.0"`
circularity_min	`"0.0"`
dbkey	`"?"`
display_results	`"no"`
exclude_edges	`"no"`
export_rois	`true`
include_holes	`"no"`
show	`"Outlines"`
size	`"2-Infinity"`

Step 17: Extract Image Features (toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.25.2+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2ae8cd6803ba55718d4d83b71ccc43a5b16aa8e6:b4d5b55c65ab800f9ea9f51426d028e465201b0e-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/519fad2c552a/2d_feature_extraction/2d_feature_extraction.py'  --labels '/tmp/tmpvdrzu6zl/files/9/c/0/dataset_9c002208-8892-43a0-8fb8-5776a9c6a482.dat'  --intensities '/tmp/tmpvdrzu6zl/files/5/1/3/dataset_51388505-430a-4215-94e8-8556e5770219.dat'  --output '/tmp/tmpvdrzu6zl/job_working_directory/000/95/outputs/dataset_289abc59-99db-4017-9c3e-59ea26559cd2.dat' --params '/tmp/tmpvdrzu6zl/job_working_directory/000/95/configs/tmp0wk_6zhk' --verbose

Exit Code:

```
0
```

Standard Output:

[labels] Input image axes: YXC
[labels] Input image shape: (600, 600, 1)
[labels] Input image dtype: uint8
[labels] Input image resolution=(1.0, 1.0), unit='inch'
[intensities] Input image axes: YXC
[intensities] Input image shape: (600, 600, 1)
[intensities] Input image dtype: float32
[intensities] Input image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
setup	`{"__current_case__": 1, "features": ["label", "mean_intensity", "area", "area_filled"], "intensities": {"values": [{"id": 91, "src": "dce"}]}, "mode": "with-intensities"}`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2ae8cd6803ba55718d4d83b71ccc43a5b16aa8e6:b4d5b55c65ab800f9ea9f51426d028e465201b0e-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/519fad2c552a/2d_feature_extraction/2d_feature_extraction.py'  --labels '/tmp/tmpvdrzu6zl/files/f/f/4/dataset_ff458793-1654-43da-8306-26105e8ff5d2.dat'  --intensities '/tmp/tmpvdrzu6zl/files/f/7/c/dataset_f7c0c296-f430-49f7-a474-91586395aa96.dat'  --output '/tmp/tmpvdrzu6zl/job_working_directory/000/96/outputs/dataset_bbc1522a-eee8-401f-ada2-24cfbb6d0472.dat' --params '/tmp/tmpvdrzu6zl/job_working_directory/000/96/configs/tmpr0pd1y7u' --verbose

Exit Code:

```
0
```

Standard Output:

[labels] Input image axes: YXC
[labels] Input image shape: (600, 600, 1)
[labels] Input image dtype: uint8
[labels] Input image resolution=(1.0, 1.0), unit='inch'
[intensities] Input image axes: YXC
[intensities] Input image shape: (600, 600, 1)
[intensities] Input image dtype: float32
[intensities] Input image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
setup	`{"__current_case__": 1, "features": ["label", "mean_intensity", "area", "area_filled"], "intensities": {"values": [{"id": 92, "src": "dce"}]}, "mode": "with-intensities"}`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2ae8cd6803ba55718d4d83b71ccc43a5b16aa8e6:b4d5b55c65ab800f9ea9f51426d028e465201b0e-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/519fad2c552a/2d_feature_extraction/2d_feature_extraction.py'  --labels '/tmp/tmpvdrzu6zl/files/6/1/4/dataset_6142c827-f4b0-4850-81c8-0ddec9a98f4c.dat'  --intensities '/tmp/tmpvdrzu6zl/files/5/5/e/dataset_55ec72ac-c0b5-4744-b6fc-0694cc2dd780.dat'  --output '/tmp/tmpvdrzu6zl/job_working_directory/000/97/outputs/dataset_72fcb2f0-de4e-4819-9db7-36efb96955ba.dat' --params '/tmp/tmpvdrzu6zl/job_working_directory/000/97/configs/tmp2n26ypiq' --verbose

Exit Code:

```
0
```

Standard Output:

[labels] Input image axes: YXC
[labels] Input image shape: (600, 600, 1)
[labels] Input image dtype: uint8
[labels] Input image resolution=(1.0, 1.0), unit='inch'
[intensities] Input image axes: YXC
[intensities] Input image shape: (600, 600, 1)
[intensities] Input image dtype: float32
[intensities] Input image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
setup	`{"__current_case__": 1, "features": ["label", "mean_intensity", "area", "area_filled"], "intensities": {"values": [{"id": 93, "src": "dce"}]}, "mode": "with-intensities"}`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2ae8cd6803ba55718d4d83b71ccc43a5b16aa8e6:b4d5b55c65ab800f9ea9f51426d028e465201b0e-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/519fad2c552a/2d_feature_extraction/2d_feature_extraction.py'  --labels '/tmp/tmpvdrzu6zl/files/c/c/c/dataset_cccaad4c-4208-43f3-a991-be5189021f60.dat'  --intensities '/tmp/tmpvdrzu6zl/files/a/b/c/dataset_abcb6b34-33d5-4f9e-81fd-168dde47a31d.dat'  --output '/tmp/tmpvdrzu6zl/job_working_directory/000/98/outputs/dataset_74d0f87b-7c2b-4fac-8501-e0f3308e188c.dat' --params '/tmp/tmpvdrzu6zl/job_working_directory/000/98/configs/tmpjszzhjg6' --verbose

Exit Code:

```
0
```

Standard Output:

[labels] Input image axes: YXC
[labels] Input image shape: (600, 600, 1)
[labels] Input image dtype: uint8
[labels] Input image resolution=(1.0, 1.0), unit='inch'
[intensities] Input image axes: YXC
[intensities] Input image shape: (600, 600, 1)
[intensities] Input image dtype: float32
[intensities] Input image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
setup	`{"__current_case__": 1, "features": ["label", "mean_intensity", "area", "area_filled"], "intensities": {"values": [{"id": 94, "src": "dce"}]}, "mode": "with-intensities"}`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2ae8cd6803ba55718d4d83b71ccc43a5b16aa8e6:b4d5b55c65ab800f9ea9f51426d028e465201b0e-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/519fad2c552a/2d_feature_extraction/2d_feature_extraction.py'  --labels '/tmp/tmpvdrzu6zl/files/a/c/4/dataset_ac4511e3-0c91-4ad6-9397-b74b8c5510e9.dat'  --intensities '/tmp/tmpvdrzu6zl/files/b/4/a/dataset_b4a6f92c-ce0c-4aef-89b0-4f5156f9802e.dat'  --output '/tmp/tmpvdrzu6zl/job_working_directory/000/99/outputs/dataset_0532acb5-f804-4e04-b602-a91872f899a5.dat' --params '/tmp/tmpvdrzu6zl/job_working_directory/000/99/configs/tmplgol6v_h' --verbose

Exit Code:

```
0
```

Standard Output:

[labels] Input image axes: YXC
[labels] Input image shape: (600, 600, 1)
[labels] Input image dtype: uint8
[labels] Input image resolution=(1.0, 1.0), unit='inch'
[intensities] Input image axes: YXC
[intensities] Input image shape: (600, 600, 1)
[intensities] Input image dtype: float32
[intensities] Input image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
setup	`{"__current_case__": 1, "features": ["label", "mean_intensity", "area", "area_filled"], "intensities": {"values": [{"id": 95, "src": "dce"}]}, "mode": "with-intensities"}`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2ae8cd6803ba55718d4d83b71ccc43a5b16aa8e6:b4d5b55c65ab800f9ea9f51426d028e465201b0e-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/519fad2c552a/2d_feature_extraction/2d_feature_extraction.py'  --labels '/tmp/tmpvdrzu6zl/files/d/9/4/dataset_d94dad0b-8c76-4d12-994b-cd54f49df863.dat'  --intensities '/tmp/tmpvdrzu6zl/files/0/e/a/dataset_0eacba73-8a4e-481d-bf23-49051ec8fe7a.dat'  --output '/tmp/tmpvdrzu6zl/job_working_directory/000/100/outputs/dataset_432363fb-28e0-49f2-bbf6-123b84d3e67b.dat' --params '/tmp/tmpvdrzu6zl/job_working_directory/000/100/configs/tmpj5yy28ku' --verbose

Exit Code:

```
0
```

Standard Output:

[labels] Input image axes: YXC
[labels] Input image shape: (600, 600, 1)
[labels] Input image dtype: uint8
[labels] Input image resolution=(1.0, 1.0), unit='inch'
[intensities] Input image axes: YXC
[intensities] Input image shape: (600, 600, 1)
[intensities] Input image dtype: float32
[intensities] Input image resolution=(1.0, 1.0), unit='inch'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
setup	`{"__current_case__": 1, "features": ["label", "mean_intensity", "area", "area_filled"], "intensities": {"values": [{"id": 96, "src": "dce"}]}, "mode": "with-intensities"}`

Step 18: Unlabelled step (Cut1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.26--2
```

Command Line:

perl '/tmp/tmpvdrzu6zl/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpvdrzu6zl/files/e/1/3/dataset_e136129c-e270-498a-a8ff-268db5864005.dat' 'c3' T '/tmp/tmpvdrzu6zl/job_working_directory/000/74/outputs/dataset_f380afcb-e573-49e4-8083-d8f888187f58.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Job 2:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.26--2
```

Command Line:

perl '/tmp/tmpvdrzu6zl/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpvdrzu6zl/files/b/f/9/dataset_bf96a9c3-37bd-43a4-9d78-5137dffd8e72.dat' 'c3' T '/tmp/tmpvdrzu6zl/job_working_directory/000/69/outputs/dataset_81bcedd4-5b8f-4203-84e0-a4f31d913243.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Job 3:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.26--2
```

Command Line:

perl '/tmp/tmpvdrzu6zl/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpvdrzu6zl/files/4/8/2/dataset_482545ad-7a6e-4d49-84ff-a6a453d6159c.dat' 'c3' T '/tmp/tmpvdrzu6zl/job_working_directory/000/70/outputs/dataset_7e6735ce-8578-4702-a370-c7015a47088b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Job 4:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.26--2
```

Command Line:

perl '/tmp/tmpvdrzu6zl/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpvdrzu6zl/files/7/b/8/dataset_7b8c38b0-1ab2-4b26-a7a2-eee02f3526c4.dat' 'c3' T '/tmp/tmpvdrzu6zl/job_working_directory/000/71/outputs/dataset_4769856f-d780-4549-b4f6-45058043364c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Job 5:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.26--2
```

Command Line:

perl '/tmp/tmpvdrzu6zl/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpvdrzu6zl/files/e/4/6/dataset_e46167a8-dc50-4838-b6d1-28b1c1ba87f4.dat' 'c3' T '/tmp/tmpvdrzu6zl/job_working_directory/000/72/outputs/dataset_48d16dea-401f-4354-952b-20e548442a85.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Job 6:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.26--2
```

Command Line:

perl '/tmp/tmpvdrzu6zl/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpvdrzu6zl/files/5/d/0/dataset_5d0a1343-9718-43e8-9c66-c8b550abdcce.dat' 'c3' T '/tmp/tmpvdrzu6zl/job_working_directory/000/73/outputs/dataset_85a73ab2-1e90-41cc-a852-e7435a5227e6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 19: Prepare Header Source Dataset (__EXTRACT_DATASET__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
input	`{"values": [{"id": 17, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 20: Extract (Show tail1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

set -eo pipefail; ( cat '/tmp/tmpvdrzu6zl/files/2/8/9/dataset_289abc59-99db-4017-9c3e-59ea26559cd2.dat' | tail -n 1 ) > '/tmp/tmpvdrzu6zl/job_working_directory/000/102/outputs/dataset_0da0a119-b8c6-4a32-9218-67fd06063e49.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

set -eo pipefail; ( cat '/tmp/tmpvdrzu6zl/files/b/b/c/dataset_bbc1522a-eee8-401f-ada2-24cfbb6d0472.dat' | tail -n 1 ) > '/tmp/tmpvdrzu6zl/job_working_directory/000/103/outputs/dataset_de1d951f-4453-431c-a062-e63a022a7a54.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Job 3:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

set -eo pipefail; ( cat '/tmp/tmpvdrzu6zl/files/7/2/f/dataset_72fcb2f0-de4e-4819-9db7-36efb96955ba.dat' | tail -n 1 ) > '/tmp/tmpvdrzu6zl/job_working_directory/000/104/outputs/dataset_004064a5-248e-4f24-b4cf-1b8f29393225.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Job 4:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

set -eo pipefail; ( cat '/tmp/tmpvdrzu6zl/files/7/4/d/dataset_74d0f87b-7c2b-4fac-8501-e0f3308e188c.dat' | tail -n 1 ) > '/tmp/tmpvdrzu6zl/job_working_directory/000/105/outputs/dataset_38933a4b-3200-4a9e-8b25-8534da7edd45.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Job 5:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

set -eo pipefail; ( cat '/tmp/tmpvdrzu6zl/files/0/5/3/dataset_0532acb5-f804-4e04-b602-a91872f899a5.dat' | tail -n 1 ) > '/tmp/tmpvdrzu6zl/job_working_directory/000/106/outputs/dataset_3a5de5bf-c257-4ebf-a73e-9ea21e5c09ef.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Job 6:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

set -eo pipefail; ( cat '/tmp/tmpvdrzu6zl/files/4/3/2/dataset_432363fb-28e0-49f2-bbf6-123b84d3e67b.dat' | tail -n 1 ) > '/tmp/tmpvdrzu6zl/job_working_directory/000/107/outputs/dataset_cf86a9ef-78f8-418f-aa3b-91c61206fcd9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Step 21: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpvdrzu6zl/job_working_directory/000/108/configs/tmpaa12uh5w' '/tmp/tmpvdrzu6zl/job_working_directory/000/108/outputs/dataset_3c10bb39-0663-4768-99eb-98ab98e01a30.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: Unlabelled step (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/gawk:5.1.0--2
```

Command Line:

(   cat "/tmp/tmpvdrzu6zl/files/8/1/b/dataset_81bcedd4-5b8f-4203-84e0-a4f31d913243.dat" ;   cat "/tmp/tmpvdrzu6zl/files/7/e/6/dataset_7e6735ce-8578-4702-a370-c7015a47088b.dat" ;   cat "/tmp/tmpvdrzu6zl/files/4/7/6/dataset_4769856f-d780-4549-b4f6-45058043364c.dat" ;   cat "/tmp/tmpvdrzu6zl/files/4/8/d/dataset_48d16dea-401f-4354-952b-20e548442a85.dat" ;   cat "/tmp/tmpvdrzu6zl/files/8/5/a/dataset_85a73ab2-1e90-41cc-a852-e7435a5227e6.dat" ;   cat "/tmp/tmpvdrzu6zl/files/f/3/8/dataset_f380afcb-e573-49e4-8083-d8f888187f58.dat" ;   ) > /tmp/tmpvdrzu6zl/job_working_directory/000/75/outputs/dataset_e1a198a5-766c-4141-8445-621801dacd42.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 23: Header Extraction (Show beginning1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

head -n 1 '/tmp/tmpvdrzu6zl/files/2/8/9/dataset_289abc59-99db-4017-9c3e-59ea26559cd2.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/109/outputs/dataset_b8179840-0301-4289-93b0-90f2d60f5748.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Step 24: Collapse Collection into one file (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/gawk:5.1.0--2
```

Command Line:

(   cat "/tmp/tmpvdrzu6zl/files/0/d/a/dataset_0da0a119-b8c6-4a32-9218-67fd06063e49.dat" ;   cat "/tmp/tmpvdrzu6zl/files/d/e/1/dataset_de1d951f-4453-431c-a062-e63a022a7a54.dat" ;   cat "/tmp/tmpvdrzu6zl/files/0/0/4/dataset_004064a5-248e-4f24-b4cf-1b8f29393225.dat" ;   cat "/tmp/tmpvdrzu6zl/files/3/8/9/dataset_38933a4b-3200-4a9e-8b25-8534da7edd45.dat" ;   cat "/tmp/tmpvdrzu6zl/files/3/a/5/dataset_3a5de5bf-c257-4ebf-a73e-9ea21e5c09ef.dat" ;   cat "/tmp/tmpvdrzu6zl/files/c/f/8/dataset_cf86a9ef-78f8-418f-aa3b-91c61206fcd9.dat" ;   ) > /tmp/tmpvdrzu6zl/job_working_directory/000/110/outputs/dataset_d7d06c0f-5894-4ec0-9442-7d5894415924.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 25: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:9.5
```

Command Line:

cat '/tmp/tmpvdrzu6zl/files/4/b/b/dataset_4bbe0e5f-52d3-4d27-8e28-b233cfec92cd.dat' >> '/tmp/tmpvdrzu6zl/job_working_directory/000/76/outputs/dataset_650ad721-32a0-4109-8936-496f7438feea.dat' && cat '/tmp/tmpvdrzu6zl/files/e/1/a/dataset_e1a198a5-766c-4141-8445-621801dacd42.dat' >> '/tmp/tmpvdrzu6zl/job_working_directory/000/76/outputs/dataset_650ad721-32a0-4109-8936-496f7438feea.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 69, "src": "hda"}]}}]`

Step 26: Paste header with Sample ID (Paste1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/7/5/f/dataset_75f8cfc6-da64-4025-9150-e7c6b31c333f.dat' '/tmp/tmpvdrzu6zl/files/b/8/1/dataset_b8179840-0301-4289-93b0-90f2d60f5748.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/111/outputs/dataset_67819a1b-bb73-48d9-ae1a-ea3cacffe799.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Step 27: Paste Sample Names with Tabular Results (Paste1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/3/c/1/dataset_3c10bb39-0663-4768-99eb-98ab98e01a30.dat' '/tmp/tmpvdrzu6zl/files/d/7/d/dataset_d7d06c0f-5894-4ec0-9442-7d5894415924.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/112/outputs/dataset_3e86d5cc-03c8-4c04-93e5-874b43a5c930.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Step 28: Tabular: Staining Feature Results (cat1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

cat '/tmp/tmpvdrzu6zl/files/6/7/8/dataset_67819a1b-bb73-48d9-ae1a-ea3cacffe799.dat' '/tmp/tmpvdrzu6zl/files/3/e/8/dataset_3e86d5cc-03c8-4c04-93e5-874b43a5c930.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/113/outputs/dataset_65e0cf7a-32a7-4163-b518-e4dd3084db18.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "input2": {"values": [{"id": 130, "src": "hda"}]}}]`

Step 29: Unlabelled step (Paste1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

paste '/tmp/tmpvdrzu6zl/files/6/5/e/dataset_65e0cf7a-32a7-4163-b518-e4dd3084db18.dat' '/tmp/tmpvdrzu6zl/files/6/5/0/dataset_650ad721-32a0-4109-8936-496f7438feea.dat' > '/tmp/tmpvdrzu6zl/job_working_directory/000/114/outputs/dataset_0e646157-0188-4ec8-b575-737ff8d15ab7.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Step 30: Percent area computation (toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/61f9ddbc63ca/column_maker/column_maker.py' --column-types str,int,float,float,float,int  --header --file '/tmp/tmpvdrzu6zl/job_working_directory/000/115/configs/tmpuex3gm7v' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpvdrzu6zl/files/0/e/6/dataset_0e646157-0188-4ec8-b575-737ff8d15ab7.dat' '/tmp/tmpvdrzu6zl/job_working_directory/000/115/outputs/dataset_2c71f1e3-c5eb-4446-85c5-7f88607773d3.dat'

Exit Code:

```
0
```

Standard Output:

c4 / c6 * 100
Computing 1 new columns with instructions ['c4 / c6 * 100;;percent_area']
Computed new column values for 100.00% of 6 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8592781c64e711f19fe13833c5e1bb43"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpvdrzu6zl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 1, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c4 / c6 * 100", "new_column_name": "percent_area"}], "header_lines_select": "yes"}`

Other invocation details
- history_id
  - 232c2c11afbb361c
- history_state
  - ok
- invocation_id
  - 232c2c11afbb361c
- invocation_state
  - scheduled
- workflow_id
  - 232c2c11afbb361c

- Update tabular output assertions to CLAHE-normalized values - Fix duplicate has_text_matching YAML key so both rows are asserted - Document the normalization step in README.md and the embedded readme

mvdbeek

This looks good to me, merging when tests pass

dianichj · 2026-06-11T10:24:59Z

Thanks a lot @mvdbeek!

Adding Normalization step to WF (CLAHE)

5bc3877

Update test expectations and docs for CLAHE normalization step

9ffd0c6

- Update tabular output assertions to CLAHE-normalized values - Fix duplicate has_text_matching YAML key so both rows are asserted - Document the normalization step in README.md and the embedded readme

mvdbeek force-pushed the staining-histologyWF-add-normalizationstep branch from 91ad9be to 9ffd0c6 Compare June 11, 2026 09:33

mvdbeek approved these changes Jun 11, 2026

View reviewed changes

mvdbeek enabled auto-merge June 11, 2026 09:35

mvdbeek merged commit 0d29d24 into main Jun 11, 2026
11 checks passed

mvdbeek deleted the staining-histologyWF-add-normalizationstep branch June 11, 2026 10:11

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Adding Normalization step to WF (CLAHE)#1256

Adding Normalization step to WF (CLAHE)#1256
mvdbeek merged 2 commits into
mainfrom
staining-histologyWF-add-normalizationstep

dianichj commented Jun 10, 2026 •

edited

Loading

Uh oh!

github-actions Bot commented Jun 10, 2026

Workflow invocation details

Uh oh!

mvdbeek left a comment

Uh oh!

Uh oh!

dianichj commented Jun 11, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

dianichj commented Jun 10, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

github-actions Bot commented Jun 10, 2026

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Uh oh!

mvdbeek left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

dianichj commented Jun 11, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

dianichj commented Jun 10, 2026 •

edited

Loading