diff featurecounts.xml @ 24:a37612abf7f9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08"

--- a/featurecounts.xml	Thu Jun 06 17:54:09 2019 -0400
+++ b/featurecounts.xml	Fri Sep 06 11:08:21 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="featurecounts" name="featureCounts" version="1.6.4" profile="16.04">
+<tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy1" profile="16.04">
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
     <requirements>
         <requirement type="package" version="1.6.4">subread</requirement>
@@ -113,7 +113,7 @@
         #end if
 
         #if $extended_parameters.R:
-            && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} *.featureCounts.bam
+            && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
         #end if
         && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
     ]]></command>
@@ -145,14 +145,15 @@
             <when value="builtin">
                 <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
                     <options from_data_table="featurecounts_anno">
-                        <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
+                        <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
                     </options>
                 </param>
             </when>
             <when value="cached">
                 <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
                     <options from_data_table="gene_sets">
-                        <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
+                        <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
+                        <filter type="sort_by" column="2" />
                     </options>
                     <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
                 </param>