Test SEACR 1.3+galaxy1 on usegalaxy.org

[natefoo]

Installed in galaxyproject/usegalaxy-tools#452

[natefoo]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1

[natefoo]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1

[mvdbeek]

Results (powered by Planemo)

Summary

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

Failed s

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

  Problems:

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1, exit_code: None, stderr: .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1, exit_code: None, stderr: .
    

  Command Line:

  Job Parameters:

  • Job parameter	Parameter value
    control_cond	{"__current_case__": 1, "control_sel": "t", "t": "0.2"}
    normalize	"true"
    mode	"stringent"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"bed"

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

  Problems:

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1, exit_code: None, stderr: .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1, exit_code: None, stderr: .
    

  Command Line:

  Job Parameters:

  • Job parameter	Parameter value
    control_cond	{"__current_case__": 1, "control_sel": "t", "t": "0.1"}
    normalize	"false"
    mode	"relaxed"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"auto"

• ❌ toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr (Test Test Prokka 1.14.6+galaxy1 #3)

  Problems:

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1, exit_code: None, stderr: .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1, exit_code: None, stderr: .
    

  Command Line:

  Job Parameters:

  • Job parameter	Parameter value
    control_cond	{"__current_case__": 0, "control_sel": "f", "f": {"values": [{"id": 88935552, "src": "hda"}]}}
    normalize	"true"
    mode	"relaxed"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"bed"

[natefoo]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr/1.3+galaxy1

Forgot to restart the first time, forgot I needed to snapshot and restart the second time...

[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/iuc/seacr/seacr (Test tool test #1)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • Calling enriched regions without control file
    Normalizing control to experimental bedgraph
    Using stringent threshold
    Creating experimental AUC file: Tue Jan  4 12:03:38 CST 2022
    Calculating optimal AUC threshold: Tue Jan  4 12:03:38 CST 2022
    Using user-provided threshold: Tue Jan  4 12:03:38 CST 2022
    Creating thresholded feature file: Tue Jan  4 12:03:47 CST 2022
    Empirical false discovery rate = 0.2
    Merging nearby features and eliminating control-enriched features: Tue Jan  4 12:03:47 CST 2022
    Removing temporary files: Tue Jan  4 12:03:47 CST 2022
    Done: Tue Jan  4 12:03:47 CST 2022
    

  Job Parameters:

  • Job parameter	Parameter value
    control_cond	{"__current_case__": 1, "control_sel": "t", "t": "0.2"}
    normalize	"true"
    mode	"stringent"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"bed"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/seacr/seacr (Test test against test.galaxyproject.org #2)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • Calling enriched regions without control file
    Proceeding without normalization of control to experimental bedgraph
    Using relaxed threshold
    Creating experimental AUC file: Tue Jan  4 12:03:38 CST 2022
    Calculating optimal AUC threshold: Tue Jan  4 12:03:38 CST 2022
    Using user-provided threshold: Tue Jan  4 12:03:38 CST 2022
    Creating thresholded feature file: Tue Jan  4 12:03:47 CST 2022
    Empirical false discovery rate = 
    Merging nearby features and eliminating control-enriched features: Tue Jan  4 12:03:47 CST 2022
    Removing temporary files: Tue Jan  4 12:03:47 CST 2022
    Done: Tue Jan  4 12:03:47 CST 2022
    

  Job Parameters:

  • Job parameter	Parameter value
    control_cond	{"__current_case__": 1, "control_sel": "t", "t": "0.1"}
    normalize	"false"
    mode	"relaxed"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"auto"

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

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • Calling enriched regions with control file
    Normalizing control to experimental bedgraph
    Using relaxed threshold
    Creating experimental AUC file: Tue Jan  4 12:03:40 CST 2022
    Creating control AUC file: Tue Jan  4 12:03:40 CST 2022
    Calculating optimal AUC threshold: Tue Jan  4 12:03:40 CST 2022
    Calculating threshold using normalized control: Tue Jan  4 12:03:40 CST 2022
    Creating thresholded feature file: Tue Jan  4 12:03:47 CST 2022
    Empirical false discovery rate = 0.181818181818182
    Merging nearby features and eliminating control-enriched features: Tue Jan  4 12:03:47 CST 2022
    Removing temporary files: Tue Jan  4 12:03:47 CST 2022
    Done: Tue Jan  4 12:03:47 CST 2022
    

  Job Parameters:

  • Job parameter	Parameter value
    control_cond	{"__current_case__": 0, "control_sel": "f", "f": {"values": [{"id": 88936436, "src": "hda"}]}}
    normalize	"true"
    mode	"relaxed"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"auto"