Mercurial > repos > iuc > qualimap_rnaseq

diff qualimap_rnaseq.xml @ 1:ce0da6c9f49e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
author: iuc
date: Tue, 29 Oct 2019 09:14:03 -0400
parents: 613e6446ea5d
--- a/qualimap_rnaseq.xml	Thu Oct 10 17:41:10 2019 -0400
+++ b/qualimap_rnaseq.xml	Tue Oct 29 09:14:03 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" version="@VERSION@">
+<tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" version="@VERSION@+galaxy1">
     <macros>
         <import>qualimap_macros.xml</import>
     </macros>
@@ -7,9 +7,13 @@
     <command detect_errors="exit_code"><![CDATA[
         @SET_JAVA_OPTS@ &&
 
+        ## Have qualimap detect file format by suffix
+        ## since its autodetection is unreliable.
+        ln -s '$features' features.gtf &&
+
         qualimap rnaseq
         -bam '${seq_info.input}'
-        -gtf '$features'
+        -gtf features.gtf
         ${seq_info.treat_as_pe}
         ${seq_info.sorted}
         ${counts_out.report_counts}