# HG changeset patch
# User greg
# Date 1481290136 18000
# Node ID 6dd02ba54da17969238fb3e5d0fc3e08deddf949
# Parent  7af9033b21a2c2255911b07e89fbd441597e236f
Deleted selected files

diff -r 7af9033b21a2 -r 6dd02ba54da1 plant_tribes_assembly_post_processor.xml
--- a/plant_tribes_assembly_post_processor.xml	Fri Dec 09 08:28:49 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,144 +0,0 @@
-<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>
-    <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 -->
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
-    <command>
-        <![CDATA[
-            AssemblyPostProcesser
-            --transcripts "$input"
-            --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($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == "yes":
-                    --gene_family_search "$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 $options_type.min_length
-                --num_threads \${GALAXY_SLOTS:-4}
-            #end if
-        ]]>
-    </command>
-    <inputs>
-        <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>
-                <option value="estscan">ESTScan</option>
-            </param>
-            <when value="transdecoder" />
-            <when value="estscan">
-                <param name="score_matrices" format="smat" type="data" label="Scores matrices"/>
-            </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 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" />
-                            <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">
-                            <option value="gfam" selected="true">GFam</option>
-                            <option value="orthofinder">OrthoFinder</option>
-                            <option value="orthomcl">OrthoMCL</option>
-                        </param>
-                    </when>
-                </conditional>
-                <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"/>
-                <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="assemblyPostProcessing_dir" visible="false" ext="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>
-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.
- * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
- * **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">
-                @unpublished{None,
-                author = {None},
-                title = {None},
-                year = {None},
-                eprint = {None},
-                url = {None}
-            }</citation>
-    </citations>
-</tool>