Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 114:2411671fdc91 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Wed, 29 Aug 2018 14:12:28 -0400
parents 233f2d346fd1
children 0d668d384a5f
comparison
equal deleted inserted replaced
113:28197cb2d6de 114:2411671fdc91
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement> 7 <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement>
8 </requirements> 8 </requirements>
9 <code file="get_clustering_methods.py"/>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #set output_dir = 'assemblyPostProcessing_dir' 11 #set output_dir = 'assemblyPostProcessing_dir'
11 AssemblyPostProcessor 12 AssemblyPostProcessor
12 --transcripts '$input' 13 --transcripts '$input'
13 --prediction_method $prediction_method_cond.prediction_method 14 --prediction_method $prediction_method_cond.prediction_method
90 <option value="yes">Yes</option> 91 <option value="yes">Yes</option>
91 </param> 92 </param>
92 <when value="no" /> 93 <when value="no" />
93 <when value="yes"> 94 <when value="yes">
94 <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/> 95 <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/>
95 <param name="scaffold" type="select" label="Gene family scaffold"> 96 <expand macro="param_scaffold"/>
96 <options from_data_table="plant_tribes_scaffolds" /> 97 <expand macro="param_method"/>
97 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
98 </param>
99 <param name="method" type="select" label="Protein clustering method">
100 <option value="gfam" selected="true">GFam</option>
101 <option value="orthofinder">OrthoFinder</option>
102 <option value="orthomcl">OrthoMCL</option>
103 </param>
104 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/> 98 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/>
105 <param name="min_coverage" type="float" value="0" min="0" max="1.0" label="Minimum alignment coverage"/> 99 <param name="min_coverage" type="float" value="0" min="0" max="1.0" label="Minimum alignment coverage"/>
106 </when> 100 </when>
107 </conditional> 101 </conditional>
108 <param name="strand_specific" type="select" label="Strand-specific assembly?"> 102 <param name="strand_specific" type="select" label="Strand-specific assembly?">