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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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test bacteria_tradis/1.4.5+galaxy2 #81

Closed jennaj closed 1 year ago

jennaj commented 1 year ago

toolshed.g2.bx.psu.edu/repos/iuc/biotradis/bacteria_tradis/1.4.5+galaxy2

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/biotradis/bacteria_tradis/1.4.5+galaxy2

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State Count
Total 2
Passed 2
Error 0
Failure 0
Skipped 0
Passed s *
✅ toolshed.g2.bx.psu.edu/repos/iuc/biotradis/bacteria_tradis (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console :::::::::::::::::: /corral4/main/objects/d/e/e/dataset_dee70ac0-7e6b-455a-a75e-cce624566348.dat :::::::::::::::::: ..........Tagless mode selected skipping steps 1 and 2 ..........Step 3: Map file to reference using bwa ..........Step 3.5: Convert output from SAM to BAM and sort ..........Step 4: Generate plot ..........Step 5: Generate statistics ..........Step 6: Move files to current directory ..........Clean up ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | map\_parameters | ` {"__current_case__": 1, "map_options": "default"} ` | | tranposon\_tag | ` {"__current_case__": 1, "use": false} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "fastq" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/biotradis/bacteria_tradis (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console :::::::::::::::::: /corral4/main/objects/d/e/e/dataset_dee70ac0-7e6b-455a-a75e-cce624566348.dat :::::::::::::::::: ..........Tagless mode selected skipping steps 1 and 2 ..........Step 3: Map file to reference using bwa ..........Step 3.5: Convert output from SAM to BAM and sort ..........Step 4: Generate plot ..........Step 5: Generate statistics ..........Step 6: Move files to current directory ..........Clean up ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | map\_parameters | ` {"__current_case__": 0, "duplicate_reads": true, "map_options": "modify", "min_percentage": "0.5", "min_quality": "20", "set_kmers_options": {"__current_case__": 0, "kmer_length": "10", "set": true, "step_size": "5"}} ` | | tranposon\_tag | ` {"__current_case__": 1, "use": false} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "fastq" ` |