# HG changeset patch
# User jjohnson
# Date 1633978845 0
# Node ID 1a56888ddb7d2fe9d58831dc45d98673c6590afb
# Parent  25d207f7ff836d0c07ce6b3886c4ec4c608ecac4
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit f5af83950615d8c77a3a43cf45f5ddf46000701b"

diff -r 25d207f7ff83 -r 1a56888ddb7d arriba.xml
--- a/arriba.xml	Mon Oct 11 16:40:51 2021 +0000
+++ b/arriba.xml	Mon Oct 11 19:00:45 2021 +0000
@@ -7,8 +7,10 @@
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
 #if str($input_params.input_source) == "use_fastq"
+    #set $readFilesCommand = ''
     #if $input_params.left_fq.is_of_type("fastq.gz"):
         #set read1 = 'input_1.fastq.gz'
+        #set $readFilesCommand = '--readFilesCommand zcat'
     #else:
         #set read1 = 'input_1.fastq'
     #end if
@@ -27,7 +29,7 @@
     --genomeDir $star_index_dir
     --genomeLoad NoSharedMemory 
     --readFilesIn $read1 $read2
-    --readFilesCommand zcat 
+    $readFilesCommand
     --outStd BAM_Unsorted 
     --outSAMtype BAM Unsorted 
     --outSAMunmapped Within