Test gffread 2.2.1.3+galaxy0

[natefoo]

Installed in galaxyproject/usegalaxy-tools#453.

[natefoo]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	10
Passed	10
Error	0
Failure	0
Skipped	0

Passed s

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

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 0, "region_filter": "none"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 0, "source": "none"}
    gffs	{"__current_case__": 1, "ensembl": "false", "gff_fmt": "gff", "tname": ""}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 0, "region_filter": "none"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 0, "source": "none"}
    gffs	{"__current_case__": 1, "ensembl": "false", "gff_fmt": "gff", "tname": ""}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 0, "region_filter": "none"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 0, "source": "none"}
    gffs	{"__current_case__": 1, "ensembl": "false", "gff_fmt": "gff", "tname": ""}
    full_gff_attribute_preservation	"true"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 0, "region_filter": "none"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 0, "source": "none"}
    gffs	{"__current_case__": 3, "gff_fmt": "bed"}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 0, "region_filter": "none"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 0, "source": "none"}
    gffs	{"__current_case__": 1, "ensembl": "false", "gff_fmt": "gff", "tname": "track name"}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 1, "discard_partial": "false", "range": "19:496500..504965", "region_filter": "filter"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 0, "source": "none"}
    gffs	{"__current_case__": 2, "gff_fmt": "gtf", "tname": ""}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test Test pangolin 3.1.17+galaxy1 #7)

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 1, "discard_partial": "true", "range": "19:496500..504965", "region_filter": "filter"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 0, "source": "none"}
    gffs	{"__current_case__": 2, "gff_fmt": "gtf", "tname": ""}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

  Command Line:

  Exit Code:

  • 0

  Job Parameters:

  • Job parameter	Parameter value
    filtering	"-C"
    region	{"__current_case__": 1, "discard_partial": "false", "range": "19:496500..504965", "region_filter": "filter"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 0, "source": "none"}
    gffs	{"__current_case__": 2, "gff_fmt": "gtf", "tname": ""}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test Test gffread 2.2.1.3+galaxy0 #9)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • FASTA index file genomeref.fa.fai created.
    

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 1, "discard_partial": "false", "range": "19:496500..504965", "region_filter": "filter"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 2, "fa_outputs": ["-w exons.fa", "-x cds.fa", "-y pep.fa"], "genome_fasta": {"values": [{"id": 88938569, "src": "hda"}]}, "ref_filtering": null, "source": "history"}
    gffs	{"__current_case__": 2, "gff_fmt": "gtf", "tname": ""}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread (Test Test trim_galore 0.6.7+galaxy0 #10)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • FASTA index file genomeref.fa.fai created.
    

  Job Parameters:

  • Job parameter	Parameter value
    filtering	None
    region	{"__current_case__": 0, "region_filter": "none"}
    maxintron	""
    chr_replace	None
    merging	{"__current_case__": 0, "merge_sel": "none"}
    reference_genome	{"__current_case__": 2, "fa_outputs": ["-y pep.fa", "-S"], "genome_fasta": {"values": [{"id": 88938569, "src": "hda"}]}, "ref_filtering": null, "source": "history"}
    gffs	{"__current_case__": 0, "gff_fmt": "none"}
    full_gff_attribute_preservation	"false"
    decode_url	"false"
    expose	"false"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"