# HG changeset patch
# User greg
# Date 1508935171 14400
# Node ID 126430ebebf76826f92f948867e0fd28fce7c2ad
# Parent  b5aac0d2c99c397baab802c5b8e572e789ac414c
Uploaded

diff -r b5aac0d2c99c -r 126430ebebf7 assembly_post_processor.xml
--- a/assembly_post_processor.xml	Wed Oct 25 08:17:33 2017 -0400
+++ b/assembly_post_processor.xml	Wed Oct 25 08:39:31 2017 -0400
@@ -7,7 +7,8 @@
         <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-python '$__tool_directory__/assembly_post_processor.py'
+#set output_dir = 'assemblyPostProcessing_dir'
+AssemblyPostProcessor
 --transcripts '$input'
 --prediction_method $prediction_method_cond.prediction_method
 #if str($prediction_method_cond.prediction_method) == 'estscan':
@@ -21,23 +22,29 @@
         --method '$target_gene_family_assembly_cond.method'
         --gap_trimming $target_gene_family_assembly_cond.gap_trimming
         --min_coverage $target_gene_family_assembly_cond.min_coverage
-        --output_targeted_gene_families_stats '$output_targeted_gene_families_stats'
     #end if
     #if str($options_type.strand_specific) == 'yes':
         --strand_specific true
     #end if
     #if str($options_type.dereplicate) == 'yes':
         --dereplicate true
-        --output_cleaned_nr_cds '$output_cleaned_nr_cds'
-        --output_cleaned_nr_pep '$output_cleaned_nr_pep'
     #end if
     --min_length $options_type.min_length
 #end if
 --num_threads \${GALAXY_SLOTS:-4}
---output_cds '$output_cds'
---output_cleaned_cds '$output_cleaned_cds'
---output_cleaned_pep '$output_cleaned_pep'
---output_pep '$output_pep'
+&& mv $output_dir/transcripts.cds '$output_cds'
+&& mv $output_dir/transcripts.pep '$output_pep'
+&& mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
+&& mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
+#if str($options_type.options_type_selector) == 'advanced':
+    #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
+        && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
+    #end if
+    #if str($options_type.dereplicate) == 'yes':
+        && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
+        && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
+    #end if
+#end if
     ]]></command>
     <inputs>
         <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>