Mercurial > repos > greg > assembly_post_processor

diff assembly_post_processor.xml @ 7:4d82da0ca014 draft

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author greg
date Mon, 30 Jan 2017 11:03:42 -0500
parents bf355f832557
children e5110df5314b
line wrap: on
line diff
--- a/assembly_post_processor.xml	Mon Jan 30 09:23:36 2017 -0500
+++ b/assembly_post_processor.xml	Mon Jan 30 11:03:42 2017 -0500
@@ -100,29 +100,28 @@
             <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" />
+                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta" compare="contains"/>
+                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
             </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="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.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.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.pep" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
+                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
             </output_collection>
         </test>
-        -->
     </tests>
     <help>
 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of