# HG changeset patch
# User greg
# Date 1480444712 18000
# Node ID 6655e5f6736b5194a741a9dbe083cead2a61c385
# Parent  32ade191a090ab29859026525fa1c643d019fa2f
Uploaded

diff -r 32ade191a090 -r 6655e5f6736b plant_tribes_assembly_post_processor.xml
--- a/plant_tribes_assembly_post_processor.xml	Tue Nov 29 09:09:12 2016 -0500
+++ b/plant_tribes_assembly_post_processor.xml	Tue Nov 29 13:38:32 2016 -0500
@@ -1,5 +1,5 @@
-<tool id="plant_tribes_assembly_post_processor" name="PlantTribes Assembly Post Processor" version="1.0.0">
-    <description></description>
+<tool id="plant_tribes_assembly_post_processor" name="PlantTribes AssemblyPostProcessor" version="1.0.0">
+    <description>pipeline</description>
     <requirements>
         <requirement type="package" version="0.2">plant_tribes_assembly_post_processor</requirement>
     </requirements>
@@ -13,7 +13,7 @@
     <command>
         <![CDATA[
             AssemblyPostProcesser
-            --transcripts "$input1"
+            --transcripts "$input"
             --prediction_method $prediction_method_cond.prediction_method
             #if str($prediction_method_cond.prediction_method) == 'estscan':
                 --score_matrices "$score_matrices"
@@ -37,7 +37,7 @@
         ]]>
     </command>
     <inputs>
-        <param name="input1" format="fasta" type="data" label="De novo transcriptome assembly fasta file"/>
+        <param name="input" format="fasta" type="data" label="De novo transcriptome assembly fasta file"/>
         <conditional name="prediction_method_cond">
             <param name="prediction_method" type="select" label="Prediction method for coding regions">
                 <option value="transdecoder" selected="true">TransDecoder</option>
@@ -45,6 +45,7 @@
             </param>
             <when value="transdecoder" />
             <when value="estscan">
+                <!-- TODO: this may require support for a new "smat" datatype -->
                 <param name="score_matrices" format="tabular" type="data" label="Scores matrices which reflect the codons preferences in the studied organisms"/>
             </when>
         </conditional>
@@ -62,10 +63,9 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <!-- TODO: this may require support for a new "smat" datatype -->
                         <param name="orthogroups" format="tabular" type="data" label="List of orthogroup identifiers for target gene families to assemble"/>
                         <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
-                            <options from_data_table="plant_tribes_scaffolds" column="2" />
+                            <options from_data_table="plant_tribes_scaffolds" />
                             <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
                         </param>
                         <param name="method" type="select" label="Protein clustering method">
@@ -90,13 +90,46 @@
     </inputs>
     <outputs>
         <collection name="transcripts" type="list">
-            <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="false" />
+            <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="false" format="fasta"/>
         </collection>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="assembly.fasta" ftype="fasta" />
+            <param name="prediction_method" value="transdecoder"/>
+            <param name="target_gene_family_assembly" value="no"/>
+            <param name="strand_specific" value="yes"/>
+            <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" />
+            </output_collection>
+        </test>
     </tests>
     <help>
-Assemblyr Post Processor pipeline
+This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
+complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It post-processes de novo assembly
+transcripts into putative coding sequences and their corresponding amino acid translations.
+
+-----
+
+**Options**
+
+ * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
+ * **Target gene family assembly?** - Select yes to target gene families to assemble.
+ * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.  The next version of this tool will use a dynamic select list for this feature.
+ * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
+ * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
+ * **Remove gappy sites in alignments** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
+ * **De novo transcriptome assembly was performed with strand-specific library?** - Select yes if de novo transcriptome assembly was performed with strand-specific library.
+ * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
+ * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.
+ 
     </help>
     <citations>
             <citation type="bibtex">