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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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Test gffread 2.2.1.3+galaxy0 #9

Closed natefoo closed 2 years ago

natefoo commented 2 years ago

Installed in galaxyproject/usegalaxy-tools#453.

natefoo commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 10
Passed 10
Error 0
Failure 0
Skipped 0
Passed s *
✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 0, "region_filter": "none"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 0, "source": "none"} ` | | gffs | ` {"__current_case__": 1, "ensembl": "false", "gff_fmt": "gff", "tname": ""} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 0, "region_filter": "none"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 0, "source": "none"} ` | | gffs | ` {"__current_case__": 1, "ensembl": "false", "gff_fmt": "gff", "tname": ""} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #3)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 0, "region_filter": "none"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 0, "source": "none"} ` | | gffs | ` {"__current_case__": 1, "ensembl": "false", "gff_fmt": "gff", "tname": ""} ` | | full\_gff\_attribute\_preservation | ` "true" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #4)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 0, "region_filter": "none"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 0, "source": "none"} ` | | gffs | ` {"__current_case__": 3, "gff_fmt": "bed"} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #5)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 0, "region_filter": "none"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 0, "source": "none"} ` | | gffs | ` {"__current_case__": 1, "ensembl": "false", "gff_fmt": "gff", "tname": "track name"} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #6)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 1, "discard_partial": "false", "range": "19:496500..504965", "region_filter": "filter"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 0, "source": "none"} ` | | gffs | ` {"__current_case__": 2, "gff_fmt": "gtf", "tname": ""} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #7)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 1, "discard_partial": "true", "range": "19:496500..504965", "region_filter": "filter"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 0, "source": "none"} ` | | gffs | ` {"__current_case__": 2, "gff_fmt": "gtf", "tname": ""} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #8)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` "-C" ` | | region | ` {"__current_case__": 1, "discard_partial": "false", "range": "19:496500..504965", "region_filter": "filter"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 0, "source": "none"} ` | | gffs | ` {"__current_case__": 2, "gff_fmt": "gtf", "tname": ""} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #9)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console FASTA index file genomeref.fa.fai created. ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 1, "discard_partial": "false", "range": "19:496500..504965", "region_filter": "filter"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 2, "fa_outputs": ["-w exons.fa", "-x cds.fa", "-y pep.fa"], "genome_fasta": {"values": [{"id": 88938569, "src": "hda"}]}, "ref_filtering": null, "source": "history"} ` | | gffs | ` {"__current_case__": 2, "gff_fmt": "gtf", "tname": ""} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test #10)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console FASTA index file genomeref.fa.fai created. ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filtering | ` None ` | | region | ` {"__current_case__": 0, "region_filter": "none"} ` | | maxintron | ` "" ` | | chr\_replace | ` None ` | | merging | ` {"__current_case__": 0, "merge_sel": "none"} ` | | reference\_genome | ` {"__current_case__": 2, "fa_outputs": ["-y pep.fa", "-S"], "genome_fasta": {"values": [{"id": 88938569, "src": "hda"}]}, "ref_filtering": null, "source": "history"} ` | | gffs | ` {"__current_case__": 0, "gff_fmt": "none"} ` | | full\_gff\_attribute\_preservation | ` "false" ` | | decode\_url | ` "false" ` | | expose | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |