Mercurial > repos > elixir-it > somaticsniper

diff somatic_sniper.xml @ 2:f7d69881bdec draft default tip

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author elixir-it
date Sat, 21 Sep 2019 13:22:28 -0400
parents 70999d19997f
children
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--- a/somatic_sniper.xml	Mon Jul 02 11:37:26 2018 -0400
+++ b/somatic_sniper.xml	Sat Sep 21 13:22:28 2019 -0400
@@ -19,7 +19,7 @@
 
 	
   ## BUILD SOMATICSNIPER COMMAND LINE 
-  \$CONDA_DEFAULT_ENV/bin/bam-somaticsniper
+  bam-somaticsniper
     -F vcf
     -q $advancedsettings.q
     -Q $advancedsettings.Q
@@ -83,7 +83,7 @@
 			</param>
 			<when value="cached">
 				<param name="index" type="select" label="Reference Genome File" >
-					<options from_data_table="all_fasta" />
+					<options from_data_table="sniper_index" />
 				</param>
       			</when>
       			<when value="history">
@@ -118,5 +118,8 @@
         </tests>
 	<help>
 		http://gmt.genome.wustl.edu/packages/somatic-sniper/
+
+this wrapper was developed from https://github.com/morinlab/tools-morinlab/tree/master/tools/somatic_sniper only the requirement and part of the command line have been changed in order to make it suitable for CONDA
+
 	</help>
 </tool>