test gubbins/3.2.1+galaxy0

[jennaj]

toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/3.2.1+galaxy0

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/3.2.1+galaxy0

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	5
Passed	5
Error	0
Failure	0
Skipped	0

Passed s

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    outfiles	["ftree", "gff", "vcf"]
    adv	{"converge_method": "weighted_robinson_foulds", "extensive_search": false, "iterations": "5", "outgroup": ""}
    really_adv	{"filter_percentage": "25.0", "max_window_size": "10000", "min_snps": "3", "min_window_size": "100", "p_value": "0.05", "remove_identical_sequences": false, "tree_builder": "raxml", "trimming_ratio": "1.0"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    outfiles	["ftree", "gff", "vcf"]
    adv	{"converge_method": "weighted_robinson_foulds", "extensive_search": false, "iterations": "3", "outgroup": ""}
    really_adv	{"filter_percentage": "25.0", "max_window_size": "10000", "min_snps": "3", "min_window_size": "100", "p_value": "0.05", "remove_identical_sequences": false, "tree_builder": "raxml", "trimming_ratio": "1.0"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    outfiles	["ftree", "gff", "vcf"]
    adv	{"converge_method": "recombination", "extensive_search": false, "iterations": "5", "outgroup": ""}
    really_adv	{"filter_percentage": "25.0", "max_window_size": "10000", "min_snps": "3", "min_window_size": "100", "p_value": "0.05", "remove_identical_sequences": false, "tree_builder": "raxml", "trimming_ratio": "1.0"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    outfiles	["gff", "vcf", "ftree", "recomb_embl", "fpoly", "ppoly", "stats", "baseb"]
    adv	{"converge_method": "recombination", "extensive_search": false, "iterations": "5", "outgroup": ""}
    really_adv	{"filter_percentage": "25.0", "max_window_size": "10000", "min_snps": "3", "min_window_size": "100", "p_value": "0.05", "remove_identical_sequences": false, "tree_builder": "raxml", "trimming_ratio": "1.0"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    outfiles	["ftree", "gff", "vcf", "recomb_embl", "fpoly", "ppoly", "stats", "baseb"]
    adv	{"converge_method": "weighted_robinson_foulds", "extensive_search": false, "iterations": "5", "outgroup": ""}
    really_adv	{"filter_percentage": "25.0", "max_window_size": "10000", "min_snps": "3", "min_window_size": "100", "p_value": "0.05", "remove_identical_sequences": true, "tree_builder": "fasttree", "trimming_ratio": "1.0"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"