# HG changeset patch
# User greg
# Date 1495462320 14400
# Node ID 5c221f721b95e4d29a957c51622ddce517ac63ed
# Parent  9a105e8f08e55d100ab32a690255d81e712cd7bf
Uploaded

diff -r 9a105e8f08e5 -r 5c221f721b95 assembly_post_processor.xml
--- a/assembly_post_processor.xml	Mon May 22 10:11:50 2017 -0400
+++ b/assembly_post_processor.xml	Mon May 22 10:12:00 2017 -0400
@@ -13,9 +13,11 @@
                 --score_matrices '$score_matrices'
             #end if
             #if str($options_type.options_type_selector) == 'advanced':
-                #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
+                #if str($) == 'yes':
                     #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
                     --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
+                    --output_pttgf $output_pttgf
+                    --output_pttgf_dir $output_pttgf.files_path
                     --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
                     --method '$target_gene_family_assembly_cond.method'
                     --gap_trimming $target_gene_family_assembly_cond.gap_trimming
@@ -83,6 +85,9 @@
         </conditional>
     </inputs>
     <outputs>
+        <data name="output_pttgf" format="pttgf" label="${tool.name} (targeted gene families) on ${on_string}">
+            <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
+        </data>
         <collection name="transcripts" type="list">
             <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="true" ext="fasta" />
         </collection>
@@ -100,18 +105,17 @@
         </test>
         <test>
             <param name="input" value="assembly.fasta" ftype="fasta" />
-            <param name="prediction_method" value="transdecoder" />
+            <param name="prediction_method" value="estscan" />
+            <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/>
             <param name="options_type_selector" value="advanced" />
-            <param name="gap_trimming" value="0.1" />
             <param name="dereplicate" value="yes" />
-            <param name="min_length" value="200" />
             <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.cds" file="transcripts2.cds" ftype="fasta"/>
+                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
                 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
                 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
-                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
-                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
+                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
+                <element name="transcripts.pep" file="transcripts2.pep" ftype="fasta"/>
             </output_collection>
         </test>
     </tests>