Test gops_coverage_1 1.0.0

[jennaj]

All GOPS tools except for "Join" are failing with a metadata error at org. With both bed and interval input/outputs.

toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0

Ref: https://help.galaxyproject.org/t/error-galaxy-set-metadata-command-not-found/7551

Test history: https://usegalaxy.org/u/jen/h/test-gops

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0

[mvdbeek]

Results (powered by Planemo)

Summary

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

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test tool test #1)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /corral4/main/jobs/041/228/41228210/galaxy_41228210.sh: line 123: galaxy-set-metadata: command not found
    

  Job Parameters:

  • Job parameter	Parameter value
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"bed"

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test test against test.galaxyproject.org #2)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /corral4/main/jobs/041/228/41228196/galaxy_41228196.sh: line 123: galaxy-set-metadata: command not found
    

  Job Parameters:

  • Job parameter	Parameter value
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"bed"

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test Test Prokka 1.14.6+galaxy1 #3)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /corral4/main/jobs/041/228/41228201/galaxy_41228201.sh: line 123: galaxy-set-metadata: command not found
    

  Standard Output:

  • Skipped 1 invalid lines of 1st dataset, 1st line #9: "chrM	4294967295	4294967322	EAS38_1_45_638_677	2	+
    ", problem: 4294967295 is larger than the size of this BitSet (536870912).
    

  Job Parameters:

  • Job parameter	Parameter value
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"bed"

[jennaj]

Technically "successful" with that same metadata error. Same as in the test history and reports from user's examined.

We should fix this before the Smorg if possible

confirmed by @mvdbeek -- needs "set-metadata script reinstalled"

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0

[mvdbeek]

Results (powered by Planemo)

Summary

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

Errored s

• ❌ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test test against test.galaxyproject.org #2)

  Execution Problem:

  • The attributes of this dataset are not properly set. Click the pencil icon in the history item to set the chrom, start, end and strand columns.
    

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test tool test #1)

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"bed"

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test Test Prokka 1.14.6+galaxy1 #3)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • Skipped 1 invalid lines of 1st dataset, 1st line #9: "chrM	4294967295	4294967322	EAS38_1_45_638_677	2	+
    ", problem: 4294967295 is larger than the size of this BitSet (536870912).
    

  Job Parameters:

  • Job parameter	Parameter value
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"bed"

[jennaj]

Hum, this doesn't show up at org. Just a green dataset, no warnings.

The attributes of this dataset are not properly set. Click the pencil icon in the history item to set the chrom, start, end and strand columns.

Under attributes, score is set for c4 instead of c5. I don't think that is new for this output -- it is making an interval dataset that we label as bed. c4 is a number instead of a dot or word (doesn't fit strict bed). Think that is Ok.