Updating workflows/imaging/fluorescence-nuclei-segmentation-and-counting from 0.1 to 0.2

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/imaging/fluorescence-nuclei-segmentation-and-counting. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

• toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5-2 should be updated to toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy1

The workflow release number has been updated from 0.1 to 0.2.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

• ❌ segmentation-and-counting.ga_0

  Problems:

  • Output with path /tmp/tmp0xd3ueo8/Overlay images on data 6 and data 5 outputpng__07da03dc-3c98-40fe-a64b-678ef1d4e373 different than expected, difference (using sim_size):
    ( /home/runner/work/iwc/iwc/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png v. /tmp/tmp4j080o7yoverlay_image.png )
    Files /home/runner/work/iwc/iwc/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png=50591b but /tmp/tmp4j080o7yoverlay_image.png=50483b - compare by size (delta=100) failed
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input_image:

      • step_state: scheduled

    • Step 2: toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/6c4b22ef2b81/2d_simple_filter/filter_image.py'  '/tmp/tmpk8nw5vvi/files/3/f/d/dataset_3fd89d72-488f-4eb6-8264-04af2bfd30be.dat' '/tmp/tmpk8nw5vvi/job_working_directory/000/2/outputs/dataset_eb2bffcb-9b43-4988-b31d-cd989ad5e23b.dat'  gaussian 3.0

          Exit Code:

          • 0

          Standard Error:

          • /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/6c4b22ef2b81/2d_simple_filter/filter_image.py:28: UserWarning: /tmp/tmpk8nw5vvi/job_working_directory/000/2/outputs/dataset_eb2bffcb-9b43-4988-b31d-cd989ad5e23b.dat is a low contrast image
              skimage.io.imsave(args.output.name, res, plugin='tifffile')
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0aea7cccf5cc11eeaee069a317dffa38"
            chromInfo	"/tmp/tmpk8nw5vvi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter	{"__current_case__": 0, "filter_type": "gaussian", "size": "3.0"}
            filter_type	"gaussian"
            radius	"3"

    • Step 3: toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.14.2+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/3f3783846dc0/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpk8nw5vvi/files/3/f/d/dataset_3fd89d72-488f-4eb6-8264-04af2bfd30be.dat' '/tmp/tmpk8nw5vvi/job_working_directory/000/3/outputs/dataset_60b18d54-3cfd-46a7-89c0-8ce5ba114471.dat' clahe

          Exit Code:

          • 0

          Standard Error:

          • /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:141: UserWarning: Possible precision loss when converting from float64 to uint16
              .format(dtypeobj_in, dtypeobj_out))
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0aea7cccf5cc11eeaee069a317dffa38"
            chromInfo	"/tmp/tmpk8nw5vvi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            h_type	"clahe"

    • Step 4: toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/e5c8e7e72373/2d_auto_threshold/auto_threshold.py' '/tmp/tmpk8nw5vvi/files/e/b/2/dataset_eb2bffcb-9b43-4988-b31d-cd989ad5e23b.dat' ./out.tif 'otsu' '0' '0.0' '0'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0aea7cccf5cc11eeaee069a317dffa38"
            block_size	"5"
            chromInfo	"/tmp/tmpk8nw5vvi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dark_bg	"true"
            dbkey	"?"
            invert_output	false
            th_method	{"__current_case__": 1, "block_size": "0", "method_id": "otsu", "offset": "0.0", "threshold": "0"}

    • Step 5: toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • bfconvert  -noflat '/tmp/tmpk8nw5vvi/files/6/0/b/dataset_60b18d54-3cfd-46a7-89c0-8ce5ba114471.dat' './res.png' && mv './res.png' ./result_image

          Exit Code:

          • 0

          Standard Output:

          • /tmp/tmpk8nw5vvi/files/6/0/b/dataset_60b18d54-3cfd-46a7-89c0-8ce5ba114471.dat
            TiffDelegateReader initializing /tmp/tmpk8nw5vvi/files/6/0/b/dataset_60b18d54-3cfd-46a7-89c0-8ce5ba114471.dat
            Reading IFDs
            Populating metadata
            Checking comment style
            Populating OME metadata
            [Tagged Image File Format] -> ./res.png [Animated PNG]
            	Converted 1/1 planes (100%)
            [done]
            0.683s elapsed (6.0+70.0ms per plane, 603ms overhead)
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0aea7cccf5cc11eeaee069a317dffa38"
            bigtiff	false
            channel_options	{"__current_case__": 0, "extract": "False"}
            chromInfo	"/tmp/tmpk8nw5vvi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            compression	"False"
            crop_options	{"__current_case__": 0, "extract": "False"}
            dbkey	"?"
            noflat	true
            out_format	"png"
            pyramid_options	{"__current_case__": 1, "generate": "False"}
            range_options	{"__current_case__": 0, "extract": "False"}
            series_options	{"__current_case__": 0, "extract": "False"}
            tile_options	{"__current_case__": 0, "extract": "False"}
            timepoint_options	{"__current_case__": 0, "extract": "False"}
            z_options	{"__current_case__": 0, "extract": "False"}

    • Step 6: toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/984358e43242/binary2labelimage/binary2label.py' '/tmp/tmpk8nw5vvi/files/1/7/1/dataset_171d8705-f607-45d0-803d-90ad5aa99202.dat' '/tmp/tmpk8nw5vvi/job_working_directory/000/6/outputs/dataset_d89ba589-5200-4a3a-bb79-b963f7a42059.dat'

          Exit Code:

          • 0

          Standard Error:

          • /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:137: UserWarning: Possible sign loss when converting negative image of type int64 to positive image of type uint16.
              .format(dtypeobj_in, dtypeobj_out))
            /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:190: UserWarning: Downcasting int64 to uint16 without scaling because max value 20 fits in uint16
              "value {} fits in {}".format(a.dtype, dtype, a.max(), dtype))
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tiff"
            __workflow_invocation_uuid__	"0aea7cccf5cc11eeaee069a317dffa38"
            chromInfo	"/tmp/tmpk8nw5vvi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode	{"__current_case__": 0, "mode_selector": "cca"}

    • Step 7: toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/002f7bad3e82/overlay_images/overlay_images.py' '/tmp/tmpk8nw5vvi/files/1/1/2/dataset_11299efa-49fe-4249-b1db-af5a7735fbc7.dat' '/tmp/tmpk8nw5vvi/files/d/8/9/dataset_d89ba589-5200-4a3a-bb79-b963f7a42059.dat' ./output.png --method seg_contour --thickness 2 --color '#ff0000' --show_label --label_color '#ffff00'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0aea7cccf5cc11eeaee069a317dffa38"
            chromInfo	"/tmp/tmpk8nw5vvi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            method_option	{"__current_case__": 2, "color": "#ff0000", "im1": {"values": [{"id": 5, "src": "hda"}]}, "im2": {"values": [{"id": 6, "src": "hda"}]}, "label_color": "#ffff00", "method": "seg_contour", "show_label": true, "thickness": "2"}

    • Step 8: toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/b58447a2eed2/count_objects/count_objects.py' '/tmp/tmpk8nw5vvi/files/d/8/9/dataset_d89ba589-5200-4a3a-bb79-b963f7a42059.dat' '/tmp/tmpk8nw5vvi/job_working_directory/000/8/outputs/dataset_af0205b8-7d39-4340-b2d6-1eeadd45b824.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tiff"
            __workflow_invocation_uuid__	"0aea7cccf5cc11eeaee069a317dffa38"
            chromInfo	"/tmp/tmpk8nw5vvi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • history_id

      • 1e1279844cf95909

    • history_state

      • ok

    • invocation_id

      • 1e1279844cf95909

    • invocation_state

      • scheduled

    • workflow_id

      • 1e1279844cf95909

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ segmentation-and-counting.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input_image:

      • step_state: scheduled

    • Step 2: toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/d51310ab328a/2d_simple_filter/filter_image.py'  '/tmp/tmps9pobh_y/files/3/c/d/dataset_3cd835ed-963b-43ec-842f-d6bc94d2fba4.dat' '/tmp/tmps9pobh_y/job_working_directory/000/2/outputs/dataset_bbe5130a-9635-4d70-b99a-7bebe0eda272.dat'  gaussian 3.0

          Exit Code:

          • 0

          Standard Error:

          • /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/d51310ab328a/2d_simple_filter/filter_image.py:29: UserWarning: /tmp/tmps9pobh_y/job_working_directory/000/2/outputs/dataset_bbe5130a-9635-4d70-b99a-7bebe0eda272.dat is a low contrast image
              skimage.io.imsave(args.output.name, res, plugin='tifffile')
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61c2cb605e311efa5fc33bd1342accd"
            chromInfo	"/tmp/tmps9pobh_y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter	{"__current_case__": 0, "filter_type": "gaussian", "size": "3.0"}
            filter_type	"gaussian"
            radius	"3"

    • Step 3: toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/b1c2c210813c/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmps9pobh_y/files/3/c/d/dataset_3cd835ed-963b-43ec-842f-d6bc94d2fba4.dat' '/tmp/tmps9pobh_y/job_working_directory/000/3/outputs/dataset_ca1c03da-4a7f-4d41-bdab-d0250fa6c102.dat' clahe

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61c2cb605e311efa5fc33bd1342accd"
            chromInfo	"/tmp/tmps9pobh_y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            h_type	"clahe"

    • Step 4: toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/699a5e9146b3/2d_auto_threshold/auto_threshold.py' '/tmp/tmps9pobh_y/files/b/b/e/dataset_bbe5130a-9635-4d70-b99a-7bebe0eda272.dat' ./out.tif 'otsu' '0' '0.0' '0'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61c2cb605e311efa5fc33bd1342accd"
            block_size	"5"
            chromInfo	"/tmp/tmps9pobh_y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dark_bg	"true"
            dbkey	"?"
            invert_output	false
            th_method	{"__current_case__": 1, "block_size": "0", "method_id": "otsu", "offset": "0.0", "threshold": "0"}

    • Step 5: toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • bfconvert  -noflat '/tmp/tmps9pobh_y/files/c/a/1/dataset_ca1c03da-4a7f-4d41-bdab-d0250fa6c102.dat' './res.png' && mv './res.png' ./result_image

          Exit Code:

          • 0

          Standard Output:

          • /tmp/tmps9pobh_y/files/c/a/1/dataset_ca1c03da-4a7f-4d41-bdab-d0250fa6c102.dat
            TiffDelegateReader initializing /tmp/tmps9pobh_y/files/c/a/1/dataset_ca1c03da-4a7f-4d41-bdab-d0250fa6c102.dat
            Reading IFDs
            Populating metadata
            Checking comment style
            Populating OME metadata
            [Tagged Image File Format] -> ./res.png [Animated PNG]
            	Converted 1/1 planes (100%)
            [done]
            0.695s elapsed (5.0+16.0ms per plane, 672ms overhead)
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61c2cb605e311efa5fc33bd1342accd"
            bigtiff	false
            channel_options	{"__current_case__": 0, "extract": "False"}
            chromInfo	"/tmp/tmps9pobh_y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            compression	"False"
            crop_options	{"__current_case__": 0, "extract": "False"}
            dbkey	"?"
            noflat	true
            out_format	"png"
            pyramid_options	{"__current_case__": 1, "generate": "False"}
            range_options	{"__current_case__": 0, "extract": "False"}
            series_options	{"__current_case__": 0, "extract": "False"}
            tile_options	{"__current_case__": 0, "extract": "False"}
            timepoint_options	{"__current_case__": 0, "extract": "False"}
            z_options	{"__current_case__": 0, "extract": "False"}

    • Step 6: toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/984358e43242/binary2labelimage/binary2label.py' '/tmp/tmps9pobh_y/files/7/3/c/dataset_73c38d32-4c30-432c-bd59-7845e7c6e9a4.dat' '/tmp/tmps9pobh_y/job_working_directory/000/6/outputs/dataset_448a66d2-48da-4f1f-9ad5-716506d73bcb.dat'

          Exit Code:

          • 0

          Standard Error:

          • /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:137: UserWarning: Possible sign loss when converting negative image of type int64 to positive image of type uint16.
              .format(dtypeobj_in, dtypeobj_out))
            /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:190: UserWarning: Downcasting int64 to uint16 without scaling because max value 20 fits in uint16
              "value {} fits in {}".format(a.dtype, dtype, a.max(), dtype))
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tiff"
            __workflow_invocation_uuid__	"d61c2cb605e311efa5fc33bd1342accd"
            chromInfo	"/tmp/tmps9pobh_y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode	{"__current_case__": 0, "mode_selector": "cca"}

    • Step 7: toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/8dc02c854048/overlay_images/overlay_images.py' '/tmp/tmps9pobh_y/files/e/9/f/dataset_e9f9a486-b3e8-4713-9c02-f2b9053abf08.dat' '/tmp/tmps9pobh_y/files/4/4/8/dataset_448a66d2-48da-4f1f-9ad5-716506d73bcb.dat' ./output.png --method seg_contour --thickness 2 --color '#ff0000' --show_label --label_color '#ffff00'

          Exit Code:

          • 1

          Standard Error:

          • Traceback (most recent call last):
              File "/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/8dc02c854048/overlay_images/overlay_images.py", line 121, in <module>
                seg_contour(args.im1, args.im2, args.out,
              File "/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/8dc02c854048/overlay_images/overlay_images.py", line 79, in seg_contour
                result = get_rgb8_copy(img)
              File "/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/8dc02c854048/overlay_images/overlay_images.py", line 41, in get_rgb8_copy
                raise ValueError(f'unknown dtype: {img.dtype}')
            ValueError: unknown dtype: int32
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61c2cb605e311efa5fc33bd1342accd"
            chromInfo	"/tmp/tmps9pobh_y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            method_option	{"__current_case__": 2, "color": "#ff0000", "im1": {"values": [{"id": 5, "src": "hda"}]}, "im2": {"values": [{"id": 6, "src": "hda"}]}, "label_color": "#ffff00", "method": "seg_contour", "show_label": true, "thickness": "2"}

    • Step 8: toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/b58447a2eed2/count_objects/count_objects.py' '/tmp/tmps9pobh_y/files/4/4/8/dataset_448a66d2-48da-4f1f-9ad5-716506d73bcb.dat' '/tmp/tmps9pobh_y/job_working_directory/000/8/outputs/dataset_276f7d57-a4d5-407a-b679-9788648c9db6.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tiff"
            __workflow_invocation_uuid__	"d61c2cb605e311efa5fc33bd1342accd"
            chromInfo	"/tmp/tmps9pobh_y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • edbe9f9bf4e5dcb1

    • history_state

      • error

    • invocation_id

      • edbe9f9bf4e5dcb1

    • invocation_state

      • scheduled

    • workflow_id

      • edbe9f9bf4e5dcb1

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

• ❌ segmentation-and-counting.ga_0

  Problems:

  • Output with path /tmp/tmp3cku1w1k/Overlay images on data 6 and data 5 outputpng__93eca535-ed13-4db1-ad40-361f09e3a586 different than expected, difference (using sim_size):
    ( /home/runner/work/iwc/iwc/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png v. /tmp/tmpxq_widqhoverlay_image.png )
    Files /home/runner/work/iwc/iwc/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png=50591b but /tmp/tmpxq_widqhoverlay_image.png=50198b - compare by size (delta=100) failed
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input_image:

      • step_state: scheduled

    • Step 2: toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/d51310ab328a/2d_simple_filter/filter_image.py'  '/tmp/tmpgnh1o55m/files/a/5/9/dataset_a59d0b93-ceb3-4591-8c64-10fe6b09cf21.dat' '/tmp/tmpgnh1o55m/job_working_directory/000/2/outputs/dataset_d316a92e-e147-44ca-927f-4c119c6628c6.dat'  gaussian 3.0

          Exit Code:

          • 0

          Standard Error:

          • /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/d51310ab328a/2d_simple_filter/filter_image.py:29: UserWarning: /tmp/tmpgnh1o55m/job_working_directory/000/2/outputs/dataset_d316a92e-e147-44ca-927f-4c119c6628c6.dat is a low contrast image
              skimage.io.imsave(args.output.name, res, plugin='tifffile')
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"308216a079bd11efaa7e056e2761212d"
            chromInfo	"/tmp/tmpgnh1o55m/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter	{"__current_case__": 0, "filter_type": "gaussian", "size": "3.0"}
            filter_type	"gaussian"
            radius	"3"

    • Step 3: toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/b1c2c210813c/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpgnh1o55m/files/a/5/9/dataset_a59d0b93-ceb3-4591-8c64-10fe6b09cf21.dat' '/tmp/tmpgnh1o55m/job_working_directory/000/3/outputs/dataset_f7d89621-32a2-4514-8d78-e00c4e3071c7.dat' clahe

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"308216a079bd11efaa7e056e2761212d"
            chromInfo	"/tmp/tmpgnh1o55m/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            h_type	"clahe"

    • Step 4: toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/699a5e9146b3/2d_auto_threshold/auto_threshold.py' '/tmp/tmpgnh1o55m/files/d/3/1/dataset_d316a92e-e147-44ca-927f-4c119c6628c6.dat' ./out.tif 'otsu' '0' '0.0' '0'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"308216a079bd11efaa7e056e2761212d"
            block_size	"5"
            chromInfo	"/tmp/tmpgnh1o55m/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dark_bg	"true"
            dbkey	"?"
            invert_output	false
            th_method	{"__current_case__": 1, "block_size": "0", "method_id": "otsu", "offset": "0.0", "threshold": "0"}

    • Step 5: toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • bfconvert  -noflat '/tmp/tmpgnh1o55m/files/f/7/d/dataset_f7d89621-32a2-4514-8d78-e00c4e3071c7.dat' './res.png' && mv './res.png' ./result_image

          Exit Code:

          • 0

          Standard Output:

          • /tmp/tmpgnh1o55m/files/f/7/d/dataset_f7d89621-32a2-4514-8d78-e00c4e3071c7.dat
            TiffDelegateReader initializing /tmp/tmpgnh1o55m/files/f/7/d/dataset_f7d89621-32a2-4514-8d78-e00c4e3071c7.dat
            Reading IFDs
            Populating metadata
            Checking comment style
            Populating OME metadata
            [Tagged Image File Format] -> ./res.png [Animated PNG]
            	Converted 1/1 planes (100%)
            [done]
            0.695s elapsed (12.0+19.0ms per plane, 662ms overhead)
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"308216a079bd11efaa7e056e2761212d"
            bigtiff	false
            channel_options	{"__current_case__": 0, "extract": "False"}
            chromInfo	"/tmp/tmpgnh1o55m/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            compression	"False"
            crop_options	{"__current_case__": 0, "extract": "False"}
            dbkey	"?"
            noflat	true
            out_format	"png"
            pyramid_options	{"__current_case__": 1, "generate": "False"}
            range_options	{"__current_case__": 0, "extract": "False"}
            series_options	{"__current_case__": 0, "extract": "False"}
            tile_options	{"__current_case__": 0, "extract": "False"}
            timepoint_options	{"__current_case__": 0, "extract": "False"}
            z_options	{"__current_case__": 0, "extract": "False"}

    • Step 6: toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/984358e43242/binary2labelimage/binary2label.py' '/tmp/tmpgnh1o55m/files/c/b/9/dataset_cb9a6fca-9ac7-4fc0-8965-e439ea57daba.dat' '/tmp/tmpgnh1o55m/job_working_directory/000/6/outputs/dataset_9019efb4-a9b9-4258-b5bb-65b2078e058d.dat'

          Exit Code:

          • 0

          Standard Error:

          • /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:137: UserWarning: Possible sign loss when converting negative image of type int64 to positive image of type uint16.
              .format(dtypeobj_in, dtypeobj_out))
            /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:190: UserWarning: Downcasting int64 to uint16 without scaling because max value 20 fits in uint16
              "value {} fits in {}".format(a.dtype, dtype, a.max(), dtype))
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tiff"
            __workflow_invocation_uuid__	"308216a079bd11efaa7e056e2761212d"
            chromInfo	"/tmp/tmpgnh1o55m/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode	{"__current_case__": 0, "mode_selector": "cca"}

    • Step 7: toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ca362a9bfa20/overlay_images/overlay_images.py' '/tmp/tmpgnh1o55m/files/f/c/2/dataset_fc25a45d-2e33-4e2e-8502-ee96a975f22b.dat' '/tmp/tmpgnh1o55m/files/9/0/1/dataset_9019efb4-a9b9-4258-b5bb-65b2078e058d.dat' ./output.png --method seg_contour --thickness 2 --color '#ff0000' --show_label --label_color '#ffff00'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"308216a079bd11efaa7e056e2761212d"
            chromInfo	"/tmp/tmpgnh1o55m/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            method_option	{"__current_case__": 2, "color": "#ff0000", "im1": {"values": [{"id": 5, "src": "hda"}]}, "im2": {"values": [{"id": 6, "src": "hda"}]}, "label_color": "#ffff00", "method": "seg_contour", "show_label": true, "thickness": "2"}

    • Step 8: toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/b58447a2eed2/count_objects/count_objects.py' '/tmp/tmpgnh1o55m/files/9/0/1/dataset_9019efb4-a9b9-4258-b5bb-65b2078e058d.dat' '/tmp/tmpgnh1o55m/job_working_directory/000/8/outputs/dataset_c877c9fd-b971-4bab-8e22-fb5fbd1ef59e.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tiff"
            __workflow_invocation_uuid__	"308216a079bd11efaa7e056e2761212d"
            chromInfo	"/tmp/tmpgnh1o55m/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • history_id

      • 7da003023243d86b

    • history_state

      • ok

    • invocation_id

      • 7da003023243d86b

    • invocation_state

      • scheduled

    • workflow_id

      • 7da003023243d86b

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

• ❌ segmentation-and-counting.ga_0

  Problems:

  • Output with path /tmp/tmprq5splph/Overlay images on data 6 and data 5 outputpng__df3775fc-3fd7-43b4-a59a-b07330a0e055 different than expected, difference (using sim_size):
    ( /home/runner/work/iwc/iwc/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png v. /tmp/tmpy0q1rpaqoverlay_image.png )
    Files /home/runner/work/iwc/iwc/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png=50591b but /tmp/tmpy0q1rpaqoverlay_image.png=50198b - compare by size (delta=100) failed
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input_image:

      • step_state: scheduled

    • Step 2: toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/d51310ab328a/2d_simple_filter/filter_image.py'  '/tmp/tmpqfhfin45/files/d/7/2/dataset_d7238992-ee45-4234-b011-b6d995c4b9ed.dat' '/tmp/tmpqfhfin45/job_working_directory/000/2/outputs/dataset_cd92f63b-f9ff-42b2-bc18-2a1c15a2dcf5.dat'  gaussian 3.0

          Exit Code:

          • 0

          Standard Error:

          • /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/d51310ab328a/2d_simple_filter/filter_image.py:29: UserWarning: /tmp/tmpqfhfin45/job_working_directory/000/2/outputs/dataset_cd92f63b-f9ff-42b2-bc18-2a1c15a2dcf5.dat is a low contrast image
              skimage.io.imsave(args.output.name, res, plugin='tifffile')
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"fbe08f047a7e11ef88c261c61f96eb03"
            chromInfo	"/tmp/tmpqfhfin45/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter	{"__current_case__": 0, "filter_type": "gaussian", "size": "3.0"}
            filter_type	"gaussian"
            radius	"3"

    • Step 3: toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/b1c2c210813c/2d_histogram_equalization/histogram_equalization.py' '/tmp/tmpqfhfin45/files/d/7/2/dataset_d7238992-ee45-4234-b011-b6d995c4b9ed.dat' '/tmp/tmpqfhfin45/job_working_directory/000/3/outputs/dataset_b847244d-5530-43cf-997f-2290f6e42fcc.dat' clahe

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"fbe08f047a7e11ef88c261c61f96eb03"
            chromInfo	"/tmp/tmpqfhfin45/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            h_type	"clahe"

    • Step 4: toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/699a5e9146b3/2d_auto_threshold/auto_threshold.py' '/tmp/tmpqfhfin45/files/c/d/9/dataset_cd92f63b-f9ff-42b2-bc18-2a1c15a2dcf5.dat' ./out.tif 'otsu' '0' '0.0' '0'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"fbe08f047a7e11ef88c261c61f96eb03"
            block_size	"5"
            chromInfo	"/tmp/tmpqfhfin45/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dark_bg	"true"
            dbkey	"?"
            invert_output	false
            th_method	{"__current_case__": 1, "block_size": "0", "method_id": "otsu", "offset": "0.0", "threshold": "0"}

    • Step 5: toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • bfconvert  -noflat '/tmp/tmpqfhfin45/files/b/8/4/dataset_b847244d-5530-43cf-997f-2290f6e42fcc.dat' './res.png' && mv './res.png' ./result_image

          Exit Code:

          • 0

          Standard Output:

          • /tmp/tmpqfhfin45/files/b/8/4/dataset_b847244d-5530-43cf-997f-2290f6e42fcc.dat
            TiffDelegateReader initializing /tmp/tmpqfhfin45/files/b/8/4/dataset_b847244d-5530-43cf-997f-2290f6e42fcc.dat
            Reading IFDs
            Populating metadata
            Checking comment style
            Populating OME metadata
            [Tagged Image File Format] -> ./res.png [Animated PNG]
            	Converted 1/1 planes (100%)
            [done]
            0.734s elapsed (9.0+21.0ms per plane, 700ms overhead)
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"fbe08f047a7e11ef88c261c61f96eb03"
            bigtiff	false
            channel_options	{"__current_case__": 0, "extract": "False"}
            chromInfo	"/tmp/tmpqfhfin45/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            compression	"False"
            crop_options	{"__current_case__": 0, "extract": "False"}
            dbkey	"?"
            noflat	true
            out_format	"png"
            pyramid_options	{"__current_case__": 1, "generate": "False"}
            range_options	{"__current_case__": 0, "extract": "False"}
            series_options	{"__current_case__": 0, "extract": "False"}
            tile_options	{"__current_case__": 0, "extract": "False"}
            timepoint_options	{"__current_case__": 0, "extract": "False"}
            z_options	{"__current_case__": 0, "extract": "False"}

    • Step 6: toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/984358e43242/binary2labelimage/binary2label.py' '/tmp/tmpqfhfin45/files/0/0/0/dataset_000f4b49-efb2-4856-aa3e-367f30256e36.dat' '/tmp/tmpqfhfin45/job_working_directory/000/6/outputs/dataset_1f2689b2-cc88-4d17-ad4a-e8a3b5c9ca81.dat'

          Exit Code:

          • 0

          Standard Error:

          • /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:137: UserWarning: Possible sign loss when converting negative image of type int64 to positive image of type uint16.
              .format(dtypeobj_in, dtypeobj_out))
            /usr/local/lib/python3.7/site-packages/skimage/util/dtype.py:190: UserWarning: Downcasting int64 to uint16 without scaling because max value 20 fits in uint16
              "value {} fits in {}".format(a.dtype, dtype, a.max(), dtype))
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tiff"
            __workflow_invocation_uuid__	"fbe08f047a7e11ef88c261c61f96eb03"
            chromInfo	"/tmp/tmpqfhfin45/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode	{"__current_case__": 0, "mode_selector": "cca"}

    • Step 7: toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ca362a9bfa20/overlay_images/overlay_images.py' '/tmp/tmpqfhfin45/files/2/5/d/dataset_25dcfec2-51c7-4b43-8405-6f44ce107b13.dat' '/tmp/tmpqfhfin45/files/1/f/2/dataset_1f2689b2-cc88-4d17-ad4a-e8a3b5c9ca81.dat' ./output.png --method seg_contour --thickness 2 --color '#ff0000' --show_label --label_color '#ffff00'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"fbe08f047a7e11ef88c261c61f96eb03"
            chromInfo	"/tmp/tmpqfhfin45/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            method_option	{"__current_case__": 2, "color": "#ff0000", "im1": {"values": [{"id": 5, "src": "hda"}]}, "im2": {"values": [{"id": 6, "src": "hda"}]}, "label_color": "#ffff00", "method": "seg_contour", "show_label": true, "thickness": "2"}

    • Step 8: toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/b58447a2eed2/count_objects/count_objects.py' '/tmp/tmpqfhfin45/files/1/f/2/dataset_1f2689b2-cc88-4d17-ad4a-e8a3b5c9ca81.dat' '/tmp/tmpqfhfin45/job_working_directory/000/8/outputs/dataset_f87e0ecc-300a-4c51-b02c-845f068ace31.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tiff"
            __workflow_invocation_uuid__	"fbe08f047a7e11ef88c261c61f96eb03"
            chromInfo	"/tmp/tmpqfhfin45/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • history_id

      • 688c14bd08cdc919

    • history_state

      • ok

    • invocation_id

      • 688c14bd08cdc919

    • invocation_state

      • scheduled

    • workflow_id

      • 688c14bd08cdc919