test custom_pro_db 1.22.0

[jennaj]

toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	3
Passed	1
Error	0
Failure	2
Skipped	0

Failed s

• ❌ toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db (Test tool test #1)

  Problems:

  • Output output_genomic_mapping_sqlite:  different than expected, difference (using diff):
    ( /tmp/tmpp_bqhaq3hg19_genomic_mapping.sqlite v. /tmp/tmptv7s7k0hhg19_genomic_mapping.sqlite )
    Binary data detected, not displaying diff
    

  • Output output_variant_annotation_sqlite:  different than expected, difference (using diff):
    ( /tmp/tmpc_allrffhg19_variant_annotation.sqlite v. /tmp/tmp68cwiwe5hg19_variant_annotation.sqlite )
    Binary data detected, not displaying diff
    

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • Loading customProDB
    Calculate RPKMs and Output proteins pass the cutoff into FASTA file ...  done
    Reading VCF file...  done
    Output variation table and variant protein sequence caused by SNVs...  done
    Output abberant protein FASTA file caused by short INDEL...  done
    

  Job Parameters:

  • Job parameter	Parameter value
    genome_annotation	{"__current_case__": 1, "bamInput": {"values": [{"id": 102810104, "src": "hda"}]}, "cosmic": null, "dbsnpInCoding": null, "exonAnno": {"values": [{"id": 102810090, "src": "hda"}]}, "ids": {"values": [{"id": 102810101, "src": "hda"}]}, "proCodingSeq": {"values": [{"id": 102810098, "src": "hda"}]}, "proteinSeq": {"values": [{"id": 102810094, "src": "hda"}]}, "source": "history", "vcfInput": {"values": [{"id": 102810108, "src": "hda"}]}}
    rpkmCutoff	"1.0"
    outputIndels	"false"
    outputSQLite	"true"
    outputRData	"true"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len"
    dbkey	"hg19"
    __input_ext	"rdata"

• ❌ toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db (Test test against test.galaxyproject.org #2)

  Problems:

  • Output output_genomic_mapping_sqlite:  different than expected, difference (using diff):
    ( /tmp/tmpilzha1m3hg19_dbsnp_genomic_mapping.sqlite v. /tmp/tmptiyd2317hg19_dbsnp_genomic_mapping.sqlite )
    Binary data detected, not displaying diff
    

  • Output output_variant_annotation_sqlite:  different than expected, difference (using diff):
    ( /tmp/tmps7iuyw9thg19_dbsnp_variant_annotation.sqlite v. /tmp/tmpid21136hhg19_dbsnp_variant_annotation.sqlite )
    Binary data detected, not displaying diff
    

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • Loading customProDB
    Calculate RPKMs and Output proteins pass the cutoff into FASTA file ...  done
    Reading VCF file...  done
    Output variation table and variant protein sequence caused by SNVs...  done
    Output abberant protein FASTA file caused by short INDEL...  done
    

  Job Parameters:

  • Job parameter	Parameter value
    genome_annotation	{"__current_case__": 1, "bamInput": {"values": [{"id": 102810104, "src": "hda"}]}, "cosmic": {"values": [{"id": 102810110, "src": "hda"}]}, "dbsnpInCoding": {"values": [{"id": 102810109, "src": "hda"}]}, "exonAnno": {"values": [{"id": 102810090, "src": "hda"}]}, "ids": {"values": [{"id": 102810101, "src": "hda"}]}, "proCodingSeq": {"values": [{"id": 102810098, "src": "hda"}]}, "proteinSeq": {"values": [{"id": 102810094, "src": "hda"}]}, "source": "history", "vcfInput": {"values": [{"id": 102810108, "src": "hda"}]}}
    rpkmCutoff	"0.0"
    outputIndels	"true"
    outputSQLite	"true"
    outputRData	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len"
    dbkey	"hg19"
    __input_ext	"rdata"

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db (Test Test Prokka 1.14.6+galaxy1 #3)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • Loading customProDB
    Calculate RPKMs and Output proteins pass the cutoff into FASTA file ...  done
    Reading VCF file...  done
    Output variation table and variant protein sequence caused by SNVs...  done
    Output abberant protein FASTA file caused by short INDEL...  done
    

  Job Parameters:

  • Job parameter	Parameter value
    genome_annotation	{"__current_case__": 1, "bamInput": {"values": [{"id": 102810104, "src": "hda"}]}, "cosmic": null, "dbsnpInCoding": null, "exonAnno": {"values": [{"id": 102810090, "src": "hda"}]}, "ids": {"values": [{"id": 102810101, "src": "hda"}]}, "proCodingSeq": {"values": [{"id": 102810098, "src": "hda"}]}, "proteinSeq": {"values": [{"id": 102810094, "src": "hda"}]}, "source": "history", "vcfInput": {"values": [{"id": 102810108, "src": "hda"}]}}
    rpkmCutoff	"1000.0"
    outputIndels	"true"
    outputSQLite	"false"
    outputRData	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len"
    dbkey	"hg19"
    __input_ext	"rdata"

[jennaj]

Maybe test case is flawed eg needs a binary diff, not plain text diff.

I ran the tutorial this morning as a broad test of the pipeline, and everything worked fine, including this tool.

https://usegalaxy.org/u/jen/h/test-customprodb