# HG changeset patch
# User iuc
# Date 1578938654 18000
# Node ID 43a1c3e1a4d00ad9d2df3cf1fd398b1b0c5d95b5
# Parent  ce0da6c9f49e8ee0bd833035afdebc6bb7c9d4e1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 3c0443b29b1fac5ec193912b0c03a79d75ba731a"

diff -r ce0da6c9f49e -r 43a1c3e1a4d0 qualimap_macros.xml
--- a/qualimap_macros.xml	Tue Oct 29 09:14:03 2019 -0400
+++ b/qualimap_macros.xml	Mon Jan 13 13:04:14 2020 -0500
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">2.2.2c</token>
+    <token name="@VERSION@">2.2.2d</token>
 
     <xml name="requirements">
         <requirements>
diff -r ce0da6c9f49e -r 43a1c3e1a4d0 test-data/rnaseq_qc_results_custom.txt
--- a/test-data/rnaseq_qc_results_custom.txt	Tue Oct 29 09:14:03 2019 -0400
+++ b/test-data/rnaseq_qc_results_custom.txt	Mon Jan 13 13:04:14 2020 -0500
@@ -3,10 +3,12 @@
 
 >>>>>>> Input
 
-    bam file = /tmp/tmp_CFvEQ/files/000/dataset_49.dat
-    gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat
+    bam file = /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmptyfj3_ok/files/a/c/2/dataset_ac26f0bf-aca4-4645-9270-5f74e2f0dffb.dat
+    gff file = features.gtf
     counting algorithm = proportional
     protocol = strand-specific-forward
+    5'-3' bias region size = 100
+    5'-3' bias number of top transcripts = 1000
 
 
 >>>>>>> Reads alignment
diff -r ce0da6c9f49e -r 43a1c3e1a4d0 test-data/rnaseq_qc_results_default.txt
--- a/test-data/rnaseq_qc_results_default.txt	Tue Oct 29 09:14:03 2019 -0400
+++ b/test-data/rnaseq_qc_results_default.txt	Mon Jan 13 13:04:14 2020 -0500
@@ -3,10 +3,12 @@
 
 >>>>>>> Input
 
-    bam file = /tmp/tmp_CFvEQ/files/000/dataset_1.dat
-    gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat
+    bam file = /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp7dpdo71_/files/7/7/6/dataset_776481e3-00ec-47dd-8143-2213c9f06699.dat
+    gff file = features.gtf
     counting algorithm = uniquely-mapped-reads
     protocol = non-strand-specific
+    5'-3' bias region size = 100
+    5'-3' bias number of top transcripts = 1000
 
 
 >>>>>>> Reads alignment