# HG changeset patch
# User greg
# Date 1485786216 18000
# Node ID bf355f8325576bfdba2fe789a15b0d30765faf23
# Parent  31673ee3734f5fc46aca0bcffd66a95214de2f2f
Uploaded

diff -r 31673ee3734f -r bf355f832557 assembly_post_processor.xml
--- a/assembly_post_processor.xml	Fri Jan 27 15:03:00 2017 -0500
+++ b/assembly_post_processor.xml	Mon Jan 30 09:23:36 2017 -0500
@@ -6,7 +6,8 @@
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
-        <!-- In case the return code has not been set properly check stderr too -->
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
         <regex match="Error:" />
         <regex match="Exception:" />
     </stdio>
@@ -21,6 +22,7 @@
             #if str($options_type.options_type_selector) == 'advanced':
                 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
                     --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups"
+                    --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
                     --scaffold "$options_type.target_gene_family_assembly_cond.scaffold"
                     --method "$options_type.target_gene_family_assembly_cond.method"
                 #end if
@@ -33,7 +35,6 @@
                 #end if
                 --min_length $options_type.min_length
             #end if
-            --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
             --num_threads \${GALAXY_SLOTS:-4}
         ]]>
     </command>
@@ -97,6 +98,18 @@
         <test>
             <param name="input" value="assembly.fasta" ftype="fasta" />
             <param name="prediction_method" value="transdecoder" />
+            <param name="options_type_selector" value="basic" />
+            <output_collection name="transcripts" type="list">
+                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" />
+                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" />
+                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta" />
+                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" />
+            </output_collection>
+        </test>
+        <!--
+        <test>
+            <param name="input" value="assembly.fasta" ftype="fasta" />
+            <param name="prediction_method" value="transdecoder" />
             <param name="options_type_selector" value="advanced" />
             <param name="strand_specific" value="yes" />
             <param name="dereplicate" value="yes" />
@@ -109,6 +122,7 @@
                 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" />
             </output_collection>
         </test>
+        -->
     </tests>
     <help>
 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of