Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.3 to 0.4

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/richard-burhans/rdeval/rdeval/0.0.7+galaxy4 should be updated to toolshed.g2.bx.psu.edu/repos/richard-burhans/rdeval/rdeval/0.0.7+galaxy5
• toolshed.g2.bx.psu.edu/repos/richard-burhans/rdeval/rdeval_report/0.0.7+galaxy4 should be updated to toolshed.g2.bx.psu.edu/repos/richard-burhans/rdeval/rdeval_report/0.0.7+galaxy5

The workflow release number has been updated from 0.3 to 0.4.

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	1
Failure	0
Skipped	0

Errored Tests

• ❌ kmer-profiling-hifi-VGP1.ga_0

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Species Name:

      • step_state: scheduled

    • Step 2: Assembly Name:

      • step_state: scheduled

    • Step 11: Unlabelled step:

      • step_state: new

    • Step 12: Unlabelled step:

      • step_state: new

    • Step 13: Unlabelled step:

      • step_state: new

    • Step 14: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 15: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 16: Homozygous Read Coverage:

      • step_state: new

    • Step 17: Estimated Genome Size:

      • step_state: new

    • Step 18: Rdeval Stats:

      • step_state: new

    • Step 19: Unlabelled step:

      • step_state: new

    • Step 3: Collection of Pacbio Data:

      • step_state: scheduled

    • Step 4: K-mer length:

      • step_state: scheduled

    • Step 5: Ploidy:

      • step_state: scheduled

    • Step 6: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dc90136607011f08b81002248aab7b6"
            chromInfo	"/tmp/tmpj9_aytgy/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Test Species", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dc90136607011f08b81002248aab7b6"
            chromInfo	"/tmp/tmpj9_aytgy/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "testSpe1", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 8: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dc90136607011f08b81002248aab7b6"
            chromInfo	"/tmp/tmpj9_aytgy/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            style_cond	{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 1, "default_value": "21", "param_type": "integer", "pick_from": [{"__index__": 0, "value": "21"}]}}

    • Step 9: Unlabelled step:

      • step_state: new

    • Step 10: Unlabelled step:

      • step_state: new
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • eae5205148a1e386

    • history_state

      • ok

    • invocation_id

      • eae5205148a1e386

    • invocation_state

      • failed

    • workflow_id

      • 665a412557e4b382