Mercurial > repos > iuc > featurecounts

changeset 23:9301937c9037 draft

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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(-) [+]
line wrap: on
line diff
--- 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&gt;&amp;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