Mercurial > repos > iuc > featurecounts
changeset 23:9301937c9037 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d
| author | iuc |
|---|---|
| date | Thu, 06 Jun 2019 17:54:09 -0400 |
| parents | af814359d244 |
| children | a37612abf7f9 |
| files | featurecounts.xml test-data/output_1_summary.tab test-data/output_summary_builtin_hg19.tab |
| diffstat | 3 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/featurecounts.xml Mon Jan 07 03:41:33 2019 -0500 +++ b/featurecounts.xml Thu Jun 06 17:54:09 2019 -0400 @@ -1,9 +1,9 @@ -<tool id="featurecounts" name="featureCounts" version="1.6.3+galaxy2" profile="16.04"> +<tool id="featurecounts" name="featureCounts" version="1.6.4" profile="16.04"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> - <requirement type="package" version="1.6.3">subread</requirement> + <requirement type="package" version="1.6.4">subread</requirement> <requirement type="package" version="1.9">samtools</requirement> - <requirement type="package" version="8.30">coreutils</requirement> + <requirement type="package" version="8.31">coreutils</requirement> </requirements> <version_command>featureCounts -v 2>&1 | grep .</version_command> @@ -297,10 +297,10 @@ <param name="mapping_quality" type="integer" - value="12" + value="0" argument="-Q" label="Minimum mapping quality per read" - help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 12 by default." /> + help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." /> <conditional name="exon_exon_junction_read_counting_enabled"> <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
--- a/test-data/output_1_summary.tab Mon Jan 07 03:41:33 2019 -0500 +++ b/test-data/output_1_summary.tab Thu Jun 06 17:54:09 2019 -0400 @@ -7,7 +7,7 @@ Unassigned_Duplicate 0 Unassigned_MultiMapping 0 Unassigned_Secondary 0 -Unassigned_Nonjunction 0 +Unassigned_NonSplit 0 Unassigned_NoFeatures 6078 Unassigned_Overlapping_Length 0 Unassigned_Ambiguity 0
--- a/test-data/output_summary_builtin_hg19.tab Mon Jan 07 03:41:33 2019 -0500 +++ b/test-data/output_summary_builtin_hg19.tab Thu Jun 06 17:54:09 2019 -0400 @@ -7,7 +7,7 @@ Unassigned_Duplicate 0 Unassigned_MultiMapping 0 Unassigned_Secondary 0 -Unassigned_Nonjunction 0 +Unassigned_NonSplit 0 Unassigned_NoFeatures 37 Unassigned_Overlapping_Length 0 Unassigned_Ambiguity 0