diff defuse.xml @ 27:d57fcac025e2

Add more info fields to defuse_results_to_vcf.py
author Jim Johnson <jj@umn.edu>
date Wed, 14 Aug 2013 16:44:18 -0500
parents 2ecf82136986
children f51a95bdc38e
line wrap: on
line diff
--- a/defuse.xml	Fri Aug 09 11:36:24 2013 -0500
+++ b/defuse.xml	Wed Aug 14 16:44:18 2013 -0500
@@ -11,6 +11,9 @@
  <inputs>
   <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads.  (FASTQ interlacer will pair reads and remove the unpaired.   FASTQ de-interlacer will separate the result into left and right reads.)"/>
   <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
+  <param name="library_name" type="text" value="unknown" label="library name" help="Value to put in the results library_name column">
+    <validator type="length" min="1"/>
+  </param>
   <conditional name="refGenomeSource">
     <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
       <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
@@ -573,7 +576,7 @@
 mkdir -p output_dir
 #end if
 ## run defuse.pl
-perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p 8
+perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p 8
 ## copy primary results to output datasets
 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi