# HG changeset patch
# User iuc
# Date 1572354843 14400
# Node ID ce0da6c9f49e8ee0bd833035afdebc6bb7c9d4e1
# Parent  613e6446ea5ddd147494eb0ed8926434b829ec1f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"

diff -r 613e6446ea5d -r ce0da6c9f49e qualimap_rnaseq.xml
--- 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}
diff -r 613e6446ea5d -r ce0da6c9f49e test-data/features.gtf
--- a/test-data/features.gtf	Thu Oct 10 17:41:10 2019 -0400
+++ b/test-data/features.gtf	Tue Oct 29 09:14:03 2019 -0400
@@ -1,3 +1,4 @@
+#comment lines (like this one) break qualimap's regions file autodetection
 test_chromosome	test	gene	1	300	.	+	.	gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
 test_chromosome	test	transcript	1	300	.	+	.	gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
 test_chromosome	test	exon	1	300	.	+	.	gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";