# HG changeset patch
# User iuc
# Date 1729748798 0
# Node ID 1b851f87fbe02ef1beee169cda8b40e28f03f7b4
# Parent  f9d49f5cb5976ccd40df320d9bd57b61b3284bb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit eb563889f227d5c473e2bad2cf9a513e41d03fca

diff -r f9d49f5cb597 -r 1b851f87fbe0 featurecounts.xml
--- a/featurecounts.xml	Sat Sep 09 21:18:37 2023 +0000
+++ b/featurecounts.xml	Thu Oct 24 05:46:38 2024 +0000
@@ -1,8 +1,8 @@
 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.0.3</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@TOOL_VERSION@">2.0.6</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."/>
@@ -15,7 +15,7 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
-        <requirement type="package" version="1.16.1">samtools</requirement>
+        <requirement type="package" version="1.21">samtools</requirement>
     </requirements>
 
     <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
@@ -627,7 +627,7 @@
   497099  chr1  3660633  3661579  -
   ======  ====  =======  =======  ======
 
-These annotation files can be found in the `Subread package`_. You can see the version of Subread used by this wrapper in the tool form above under `Options > Requirements`. To create the files, the annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the `Subread User's Guide`_ for more information. Gene names can be obtained for these Entrez identifiers with the Galaxy **annotateMyIDs** tool.
+These annotation files can be found in the _`Subread package`_. You can see the version of Subread used by this wrapper in the tool form above under `Options > Requirements`. To create the files, the annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the `Subread User's Guide`_ for more information. Gene names can be obtained for these Entrez identifiers with the Galaxy **annotateMyIDs** tool.
 
 Output format
 -------------
@@ -635,7 +635,6 @@
 
 .. _Subread: http://subread.sourceforge.net/
 .. _`Subread User's Guide`: https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf
-.. _`Subread package`: https://sourceforge.net/projects/subread/files/
     ]]></help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt656</citation>