# HG changeset patch
# User iuc
# Date 1572354860 14400
# Node ID 4a89c6f84425b5c65603002fe32598827e69258b
# Parent  ac607906f10a42e83aa7f4221814877ab772b514
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"

diff -r ac607906f10a -r 4a89c6f84425 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Thu Oct 10 17:42:04 2019 -0400
+++ b/qualimap_bamqc.xml	Tue Oct 29 09:14:20 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@">
+<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy1">
     <macros>
         <import>qualimap_macros.xml</import>
     </macros>
@@ -21,11 +21,12 @@
         ## from $out_dir.
         #set $per_base_coverage_target = $coverage_file
 
-        qualimap bamqc
-        -bam '$input1' -outdir results -outformat html
-        --collect-overlap-pairs
         #if str($stats_regions.region_select) == 'custom_regions':
-            -gff ${stats_regions.regions}
+            ## Have qualimap detect file format by suffix
+            ## since its autodetection is unreliable.
+            #set $regions_file = '.'.join(['regions', str($stats_regions.regions.ext)])
+            ln -s '${stats_regions.regions}' ${regions_file} &&
+
             #if $stats_regions.outside_stats:
                 #set $report_name = 'qualimapReportOutsideRegions'
                 #set $summary_report = 'outside_results.txt'
@@ -35,9 +36,15 @@
                 #if $per_base_coverage:
                     #set $per_base_coverage_target = '/dev/null'
                 #end if
-                ${stats_regions.outside_stats}
             #end if
         #end if
+
+        qualimap bamqc
+        -bam '$input1' -outdir results -outformat html
+        --collect-overlap-pairs
+        #if str($stats_regions.region_select) == 'custom_regions':
+            -gff ${regions_file} ${stats_regions.outside_stats}
+        #end if
         #if $per_base_coverage:
             $per_base_coverage $per_base_coverage_target
         #end if
diff -r ac607906f10a -r 4a89c6f84425 test-data/features.gtf
--- a/test-data/features.gtf	Thu Oct 10 17:42:04 2019 -0400
+++ b/test-data/features.gtf	Tue Oct 29 09:14:20 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";