# HG changeset patch
# User cmonjeau
# Date 1440430752 0
# Node ID c9e10e0d6c109a3dd817b0853c04849e8d3da08e
# Parent  ccfa8e539bdf9befc0b78675bf33ec967a9e2e39
fix discard file

diff -r ccfa8e539bdf -r c9e10e0d6c10 STACKS_procrad.py
--- a/STACKS_procrad.py	Mon Aug 24 10:09:14 2015 +0000
+++ b/STACKS_procrad.py	Mon Aug 24 15:39:12 2015 +0000
@@ -36,6 +36,7 @@
     parser.add_argument('--outype')
     parser.add_argument('--qualitenc')
     parser.add_argument('-D', action='store_true')
+    parser.add_argument('--discard_file')
     parser.add_argument('-t')
     parser.add_argument('-q', action='store_true')
     parser.add_argument('--activate_advanced_options')
diff -r ccfa8e539bdf -r c9e10e0d6c10 STACKS_procrad.xml
--- a/STACKS_procrad.xml	Mon Aug 24 10:09:14 2015 +0000
+++ b/STACKS_procrad.xml	Mon Aug 24 15:39:12 2015 +0000
@@ -53,6 +53,7 @@
     --qualitenc $options_quality.qualitenc
     #if $capture:
         -D
+        --discard_file $discard_file
     #end if
     --activate_advanced_options $activate_advanced_options
     -t $options_advanced.truncate
@@ -244,8 +245,6 @@
     <data format="fastq" name="discard_file" label="discard.fastq with ${tool.name} on ${on_string}: demultiplexed and cleaned reads ">
 	<filter>capture</filter>
     </data>
-
-
 </outputs>
 
 <stdio>
diff -r ccfa8e539bdf -r c9e10e0d6c10 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 24 10:09:14 2015 +0000
+++ b/tool_dependencies.xml	Mon Aug 24 15:39:12 2015 +0000
@@ -10,4 +10,3 @@
       <repository name="package_velvet_1_2_10" changeset_revision="1c500c3e7fdf" owner="rjullien" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu/" />
     </package>
 </tool_dependency>
-