Test Prokka 1.14.6+galaxy1

[natefoo]

EDIT: forgot the slash commands only work in comments

[natefoo]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.6+galaxy1

[mvdbeek]

Results (powered by Planemo)

Summary

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

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka (Test tool test #1)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/039/109/39109957/_job_tmp -Xmx28g -Xms256m
    Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/039/109/39109957/_job_tmp -Xmx28g -Xms256m
    

  Standard Output:

  • [tbl2asn-forever] Found Prokka input, correcting dates in .gbf|.sqn files.
    [tbl2asn-forever] Correcting dates in outdir/prokka.gbf
    [tbl2asn-forever] Correcting dates in outdir/prokka.sqn
    [tbl2asn-forever] Dates changed from 01-JAN-2019 to 17-NOV-2021
    

  Job Parameters:

  • Job parameter	Parameter value
    locustag	""
    increment	"1"
    gffver	"3"
    compliant	{"__current_case__": 0, "addgenes": "false", "compliant_select": "no", "mincontig": "200"}
    centre	""
    genus	""
    species	""
    strain	""
    plasmid	""
    kingdom	{"__current_case__": 1, "gcode": "11", "kingdom_select": "Bacteria"}
    usegenus	"false"
    proteins	None
    metagenome	"false"
    fast	"false"
    evalue	"1e-06"
    rfam	"false"
    norrna	"false"
    notrna	"false"
    outputs	["gff", "gbk", "fna", "faa", "ffn", "sqn", "fsa", "tbl", "tsv", "err", "txt"]
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fasta"