Updating workflows/epigenetics/correlation-of-samples-on-peaks from 0.1 to 0.2

[gxydevbot]

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0

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

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

• ❌ correlation-of-samples-on-peaks.ga_0

  Problems:

  • Output with path /tmp/tmpbjqmq_1v/plotCorrelation on dataset 10 Image__f02a8c86-68d2-4093-889a-3ea025ce17f5.png different than expected, difference (using diff):
    ( /home/runner/work/iwc/iwc/workflows/epigenetics/correlation-of-samples-on-peaks/test-data/correlation plot.png v. /tmp/tmpc8bb4fbgcorrelation plot.png )
    Binary data detected, not displaying diff
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Collection of peak files:

      • step_state: scheduled

    • Step 2: Reference genome:

      • step_state: scheduled

    • Step 3: BAM or CRAM files:

      • step_state: scheduled

    • Step 4: Concatenate all files into one (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/tmpw_24326e/files/5/0/b/dataset_50bc8dc4-522a-4959-bc6c-f3f45f12c28b.dat' >> '/tmp/tmpw_24326e/job_working_directory/000/5/outputs/dataset_cd294922-8e07-4a83-809d-9139d2cd2713.dat' && cat '/tmp/tmpw_24326e/files/2/9/d/dataset_29d84321-c213-49cf-852d-e3d9a6b7e546.dat' >> '/tmp/tmpw_24326e/job_working_directory/000/5/outputs/dataset_cd294922-8e07-4a83-809d-9139d2cd2713.dat' && exit 0

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"2f66efd2899911f194247ced8d078b6a"
            chromInfo	"/tmp/tmpw_24326e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            queries	[]

    • Step 5: Sort bed files (toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/bedtools:2.31.1--h13024bc_3

          Command Line:

          • sortBed -i '/tmp/tmpw_24326e/files/c/d/2/dataset_cd294922-8e07-4a83-809d-9139d2cd2713.dat'   -g '/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm39.len'  > '/tmp/tmpw_24326e/job_working_directory/000/6/outputs/dataset_4896d942-eff6-4db7-a43d-d6018859b0ec.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"2f66efd2899911f194247ced8d078b6a"
            chromInfo	"/tmp/tmpw_24326e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            genome_file_opts	{"__current_case__": 0, "genome": "mm39", "genome_file_opts_selector": "loc"}
            option	""

    • Step 6: Merge bed file (toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1+galaxy2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/bedtools:2.31.1--h13024bc_3

          Command Line:

          • mergeBed -i '/tmp/tmpw_24326e/files/4/8/9/dataset_4896d942-eff6-4db7-a43d-d6018859b0ec.dat'  -d 0    > '/tmp/tmpw_24326e/job_working_directory/000/7/outputs/dataset_86fbdee9-6ae1-4b93-b2d1-8666e1ba7219.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"2f66efd2899911f194247ced8d078b6a"
            c_and_o_argument_repeat	[]
            chromInfo	"/tmp/tmpw_24326e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            distance	"0"
            header	false
            strand	""

    • Step 7: multiBamSummary (toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1

          Command Line:

          • ln -s '/tmp/tmpw_24326e/files/4/3/1/dataset_4318319a-28e7-4857-9e5a-0e142312cc55.dat' './0.bam' && ln -s '/tmp/tmpw_24326e/files/_metadata_files/3/a/8/metadata_3a8b594f-b1c9-4a86-bcc1-9cf915f302db.dat' './0.bam.bai' && ln -s '/tmp/tmpw_24326e/files/f/7/3/dataset_f739e598-6c50-4b06-bee4-bcc44d8a3d97.dat' './1.bam' && ln -s '/tmp/tmpw_24326e/files/_metadata_files/2/d/b/metadata_2dbe886c-9788-460b-a809-2c49cd49407c.dat' './1.bam.bai' &&   multiBamSummary BED-file --numberOfProcessors "${GALAXY_SLOTS:-4}"  --outFileName '/tmp/tmpw_24326e/job_working_directory/000/8/outputs/dataset_34d8b0c6-e4b3-415c-a434-11d48a4ab6de.dat' --bamfiles '0.bam' '1.bam' --labels 'sample2' 'sample1'  --outRawCounts '/tmp/tmpw_24326e/job_working_directory/000/8/outputs/dataset_bc33ab78-936d-4392-9c77-2855cfdaaa72.dat'   --BED /tmp/tmpw_24326e/files/8/6/f/dataset_86fbdee9-6ae1-4b93-b2d1-8666e1ba7219.dat

          Exit Code:

          • 0

          Standard Error:

          • Number of bins found: 20
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"2f66efd2899911f194247ced8d078b6a"
            advancedOpt	{"__current_case__": 0, "showAdvancedOpt": "no"}
            chromInfo	"/tmp/tmpw_24326e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            custom_sample_labels_conditional	{"__current_case__": 0, "custom_labels_select": "No"}
            dbkey	"?"
            mode	{"__current_case__": 1, "modeOpt": "BED-file", "region_file": {"values": [{"id": 7, "src": "hda"}]}}
            multibam_conditional	{"__current_case__": 0, "bamfiles": {"values": [{"id": 2, "src": "hdca"}]}, "orderMatters": "No"}
            outRawCounts	true
            region	""
            scalingFactors	false

    • Step 8: Correlation plot (toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1

          Command Line:

          • plotCorrelation --corData '/tmp/tmpw_24326e/files/3/4/d/dataset_34d8b0c6-e4b3-415c-a434-11d48a4ab6de.dat' --plotFile '/tmp/tmpw_24326e/job_working_directory/000/9/outputs/dataset_f02a8c86-68d2-4093-889a-3ea025ce17f5.dat' --corMethod 'spearman' --whatToPlot 'heatmap'  --colorMap 'RdYlBu' --plotNumbers --plotTitle ''  --plotWidth 11.0 --plotHeight 9.5  --plotFileFormat 'png'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"2f66efd2899911f194247ced8d078b6a"
            chromInfo	"/tmp/tmpw_24326e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            corMethod	"spearman"
            dbkey	"?"
            outFileCorMatrix	false
            outFileFormat	"png"
            plotting_type	{"__current_case__": 0, "colorMap": "RdYlBu", "plotHeight": "9.5", "plotNumbers": true, "plotTitle": "", "plotWidth": "11.0", "whatToPlot": "heatmap", "zMax": "", "zMin": ""}
            removeOutliers	false
            skipZeros	false

  • Other invocation details

    • history_id

      • 1a36d7fff0c3f350

    • history_state

      • ok

    • invocation_id

      • 1a36d7fff0c3f350

    • invocation_state

      • scheduled

    • workflow_id

      • 1a36d7fff0c3f350