# HG changeset patch
# User greg
# Date 1479151619 18000
# Node ID e7b4a6ce3d53ca2389e7e1edfb99b2ba1f683a3b

Uploaded

diff -r 000000000000 -r e7b4a6ce3d53 plant_tribes_assembly_post_processor.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plant_tribes_assembly_post_processor.xml	Mon Nov 14 14:26:59 2016 -0500
@@ -0,0 +1,110 @@
+<tool id="plant_tribes_assembly_post_processor" name="Plant Tribes Assembly Post Processor" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="0.1">plant_tribes_assembly_post_processor</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <command>
+        <![CDATA[
+            mkdir -p output &&
+            plant_tribes_assembly_post_processor
+            --transcripts "$input1"
+            --prediction_method $prediction_method_cond.prediction_method
+            #if str($prediction_method_cond.prediction_method) == 'estscan':
+                --score_matrices "$score_matrices"
+            #end if
+            #if str($options_type.options_type_selector) == 'advanced':
+                #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == "yes":
+                    --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups"
+                    --scaffold "$options_type.target_gene_family_assembly_cond.scaffold"
+                    --method "$options_type.target_gene_family_assembly_cond.method"
+                # end if
+                --gap_trimming $options_type.gap_trimming
+                #if str($options_type.strand_specific) == 'yes':
+                    --strand_specific
+                #end if
+                #if str($options_type.dereplicate) == 'yes':
+                    --dereplicate
+                #end if
+                --min_length $min_length
+                --num_threads \${GALAXY_SLOTS:-4}
+            #end if
+        ]]>
+    </command>
+    <inputs>
+        <param name="input1" 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>
+                <option value="estscan">ESTScan</option>
+            </param>
+            <when value="transdecoder" />
+            <when value="estscan">
+                <param name="score_matrices" format="tabular" type="data" label="Scores matrices which reflect the codons preferences in the studied organisms"/>
+            </when>
+        </conditional>
+        <conditional name="options_type">
+            <param name="options_type_selector" type="select" label="Options Configuration">
+                <option value="basic" selected="true">Basic</option>
+                <option value="advanced">Advanced</option>
+            </param>
+            <when value="basic" />
+            <when value="advanced">
+                <conditional name="target_gene_family_assembly_cond">
+                    <param name="target_gene_family_assembly" type="select" label="Target gene family assembly?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param format="tabular" name="orthogroups" type="data" label="Targeted gene families (orthogroups)"/>
+                        <!-- TODO: This needs to be a scaffold file, like 22Gv1.0, 22Gv1.1, etc.  This will likely require a new datatype,
+                        but to get this to work for now I'll just use the supported fasta datatype. -->
+                        <param format="fasta" name="scaffold" type="data" label="Orthogroups or gene families proteins scaffold"/>
+                        <param name="method" type="select" label="Protein clustering method">
+                            <option value="gfam" selected="true">GFam</option>
+                            <option value="orthofinder">OrthoFinder</option>
+                            <option value="orthomcl">OrthoMCL</option>
+                        </param>
+                        <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove gappy sites in alignments" help="0.1 removes sites with 90% gaps"/>
+                    </when>
+                </conditional>
+                <param name="strand_specific" type="select" label="De novo transcriptome assembly was performed with strand-specific library?">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <param name="dereplicate" type="select" label="Remove repeated sequences in predicted coding regions?">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <param name="min_length" type="integer" value="200" label="Minimum sequence length of predicted coding regions"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="transcripts" type="list">
+            <discover_datasets pattern="__name__" directory="output" visible="false" />
+        </collection>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+Assemblyr Post Processor pipeline
+    </help>
+    <citations>
+            <citation type="bibtex">
+                @unpublished{None,
+                author = {None},
+                title = {None},
+                year = {None},
+                eprint = {None},
+                url = {None}
+            }</citation>
+    </citations>
+</tool>