test dropletutils/1.10.0+galaxy2

[jennaj]

toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	6
Passed	6
Error	0
Failure	0
Skipped	0

Passed s

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

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE,  : 
      ignoring SIGPIPE signal
    Calls: <Anonymous> -> print.numeric_version -> print -> print.default
    Execution halted
    Cells: 1025
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    tenx_format	{"__current_case__": 0, "input": {"values": [{"id": 109456188, "src": "hda"}]}, "input_barcodes": {"values": [{"id": 109456213, "src": "hda"}]}, "input_genes": {"values": [{"id": 109456199, "src": "hda"}]}, "use": "directory"}
    operation	{"__current_case__": 0, "method": {"__current_case__": 0, "expected": "3000", "lowerprop": "0.1", "upperquant": "0.99", "use": "defaultdrops"}, "outformat": "h5", "use": "filter"}
    seed	"100"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"mtx"

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

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE,  : 
      ignoring SIGPIPE signal
    Calls: <Anonymous> -> print.numeric_version -> print -> print.default
    Execution halted
    Cells: 1025
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    tenx_format	{"__current_case__": 0, "input": {"values": [{"id": 109456188, "src": "hda"}]}, "input_barcodes": {"values": [{"id": 109456213, "src": "hda"}]}, "input_genes": {"values": [{"id": 109456199, "src": "hda"}]}, "use": "directory"}
    operation	{"__current_case__": 0, "method": {"__current_case__": 0, "expected": "3000", "lowerprop": "0.1", "upperquant": "0.99", "use": "defaultdrops"}, "outformat": "tsv", "use": "filter"}
    seed	"100"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"mtx"

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

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE,  : 
      ignoring SIGPIPE signal
    Calls: <Anonymous> -> print.numeric_version -> print -> print.default
    Execution halted
    Warning message:
    In xy.coords(x, y, xlabel, ylabel, log) :
      7432 y values <= 0 omitted from logarithmic plot
    

  Standard Output:

  • [1] "knee = 324 , inflection =  151"
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    tenx_format	{"__current_case__": 0, "input": {"values": [{"id": 109456188, "src": "hda"}]}, "input_barcodes": {"values": [{"id": 109456213, "src": "hda"}]}, "input_genes": {"values": [{"id": 109456199, "src": "hda"}]}, "use": "directory"}
    operation	{"__current_case__": 1, "lower": "120", "use": "barcode_rank"}
    seed	"100"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"mtx"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils (Test Test roary 3.13.0+galaxy2 #4)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE,  : 
      ignoring SIGPIPE signal
    Calls: <Anonymous> -> print.numeric_version -> print -> print.default
    Execution halted
    Cells: 998
    Cells and Limited: 998
    

  Standard Output:

  • [1] "Cell Library Size Distribution:"
       Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
       0.00    0.00    0.00   46.53    3.00 1153.00 
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    tenx_format	{"__current_case__": 0, "input": {"values": [{"id": 109456188, "src": "hda"}]}, "input_barcodes": {"values": [{"id": 109456213, "src": "hda"}]}, "input_genes": {"values": [{"id": 109456199, "src": "hda"}]}, "use": "directory"}
    operation	{"__current_case__": 0, "method": {"__current_case__": 1, "fdr_thresh": "0.02", "lower": "150", "use": "emptydrops"}, "outformat": "h5", "use": "filter"}
    seed	"100"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"mtx"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE,  : 
      ignoring SIGPIPE signal
    Calls: <Anonymous> -> print.numeric_version -> print -> print.default
    Execution halted
    Cells: 954
    Cells and Limited: 85
    

  Standard Output:

  • [1] "Cell Library Size Distribution:"
       Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
        0.0     8.0    20.0   114.3    46.0  2347.0 
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    tenx_format	{"__current_case__": 1, "input": {"values": [{"id": 109456180, "src": "hda"}]}, "use": "h5"}
    operation	{"__current_case__": 0, "method": {"__current_case__": 1, "fdr_thresh": "0.02", "lower": "150", "use": "emptydrops"}, "outformat": "h5", "use": "filter"}
    seed	"100"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"h5"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils (Test Test trinotate 3.2.2+galaxy0 #6)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE,  : 
      ignoring SIGPIPE signal
    Calls: <Anonymous> -> print.numeric_version -> print -> print.default
    Execution halted
    Cells: 2650
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    tenx_format	{"__current_case__": 2, "input": {"values": [{"id": 109456202, "src": "hda"}]}, "use": "tsv"}
    operation	{"__current_case__": 0, "method": {"__current_case__": 0, "expected": "2000", "lowerprop": "0.1", "upperquant": "0.85", "use": "defaultdrops"}, "outformat": "directory", "use": "filter"}
    seed	"100"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"tabular"