Mercurial > repos > jjohnson > arriba

changeset 8:1a56888ddb7d draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit f5af83950615d8c77a3a43cf45f5ddf46000701b"
author jjohnson
date Mon, 11 Oct 2021 19:00:45 +0000
parents 25d207f7ff83
children 8c4c97fd0555
files arriba.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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