Mercurial > repos > sanbi-uwc > qualimap2

diff qualimap_bamqc.xml @ 6:8dff744880cd draft

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planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
author sanbi-uwc
date Tue, 05 Apr 2016 04:45:41 -0400
parents a19abfa30ca7
children
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--- a/qualimap_bamqc.xml	Tue Apr 05 03:53:28 2016 -0400
+++ b/qualimap_bamqc.xml	Tue Apr 05 04:45:41 2016 -0400
@@ -10,10 +10,10 @@
     </stdio>
     <command interpreter="python">
         qualimap_bamqc.py
-            --input_file ${input_realigned_bam_file}
-            --out_genome_file ${genomecov_file}
-            --out_dir ${genomecov_file.files_path}
-            --java_mem_size ${mem_size}
+            --input_file $input_realigned_bam_file
+            --out_genome_file $genomecov_file
+            --out_dir $genomecov_file.files_path
+            --java_mem_size $mem_size
     </command>
     <inputs>
         <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>