# HG changeset patch
# User greg
# Date 1493820851 14400
# Node ID 3227f0f39800effab596960d002aa3ad96b9cb8e
# Parent  b7858b1f64f17fa564e9687156a217b6be3a2eac
Uploaded

diff -r b7858b1f64f1 -r 3227f0f39800 assembly_post_processor.xml
--- a/assembly_post_processor.xml	Wed May 03 10:14:03 2017 -0400
+++ b/assembly_post_processor.xml	Wed May 03 10:14:11 2017 -0400
@@ -7,7 +7,7 @@
     <expand macro="stdio" />
     <command>
         <![CDATA[
-            AssemblyPostProcessor
+            python $__tool_directory__/assembly_post_processor.py
             --transcripts '$input'
             --prediction_method $prediction_method_cond.prediction_method
             #if str($prediction_method_cond.prediction_method) == 'estscan':
@@ -22,15 +22,14 @@
                     --gap_trimming $target_gene_family_assembly_cond.gap_trimming
                 #end if
                 #if str($options_type.strand_specific) == 'yes':
-                    --strand_specific
+                    --strand_specific 'true'
                 #end if
                 #if str($options_type.dereplicate) == 'yes':
-                    --dereplicate
+                    --dereplicate 'true'
                 #end if
                 --min_length $options_type.min_length
             #end if
             --num_threads \${GALAXY_SLOTS:-4}
-            >/dev/null
         ]]>
     </command>
     <inputs>