# HG changeset patch
# User iuc
# Date 1746611953 0
# Node ID 8620533d294b10814eea7d8a0b24bfe9b2d250af
# Parent  39863c075dca3c970169aaec6f8def1ab4037568
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c43e4b51d4b0a46eeba363fa4061d4af03a677a4

diff -r 39863c075dca -r 8620533d294b featurecounts.xml
--- a/featurecounts.xml	Sun Dec 22 10:54:51 2024 +0000
+++ b/featurecounts.xml	Wed May 07 09:59:13 2025 +0000
@@ -1,9 +1,8 @@
-<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
+<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.0.8</token>
+        <token name="@TOOL_VERSION@">2.1.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
-
         <macro name="conditional_gff_opions">
             <param name="gff_feature_type" type="text" value="exon" argument="-t" label="GFF feature type filter" help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default."/>
             <param name="gff_feature_attribute" type="text" value="gene_id" argument="-g" label="GFF gene identifier" help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization. Ex: if the 9th column is 'gene_id &quot;ENSG00000223972&quot;; gene_name &quot;DDX11L1&quot; gene_source &quot;havana&quot;' (GTF) or 'gene_id=ENSG00000223972; gene_name=DDX11L1; gene_source=havana' (GFF), the available attributes for this feature are 'gene_id', 'gene_name' and 'gene_source'."/>
diff -r 39863c075dca -r 8620533d294b test-data/output.bam
Binary file test-data/output.bam has changed
diff -r 39863c075dca -r 8620533d294b test-data/output_1_jcounts.tab
--- a/test-data/output_1_jcounts.tab	Sun Dec 22 10:54:51 2024 +0000
+++ b/test-data/output_1_jcounts.tab	Wed May 07 09:59:13 2025 +0000
@@ -1,1 +1,1 @@
-PrimaryGene	SecondaryGenes	Site1_chr	Site1_location	Site1_strand	Site2_chr	Site2_location	Site2_strand	featureCounts_input1.bam
+Gene_SP1	Gene_SP2	Transcript	Status	Donor	Acceptor	Chr_SP1	Location_SP1	Strand_SP1	Chr_SP2	Location_SP2	Strand_SP2	NearestExonBoundary_SP1	NearestExonBoundary_SP2	featureCounts_input1.bam
diff -r 39863c075dca -r 8620533d294b test-data/subset.sorted.featurecounts.bam
Binary file test-data/subset.sorted.featurecounts.bam has changed