Mercurial > repos > greg > plant_tribes_gene_family_classifier

comparison gene_family_classifier.xml @ 6:e813f9537cb2 draft

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author greg
date Thu, 30 Aug 2018 09:43:24 -0400
parents fd170580a6c9
children 0916fe9ef46f
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5:fd170580a6c9 6:e813f9537cb2
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_gene_family_classifier</requirement> 7 <requirement type="package" version="1.0.3">plant_tribes_gene_family_classifier</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 #if str($options_type.options_type_selector) == 'advanced': 11 #if str($options_type.options_type_selector) == 'advanced':
11 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond 12 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
12 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups 13 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
13 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 14 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
89 #end if 90 #end if
90 ]]></command> 91 ]]></command>
91 <inputs> 92 <inputs>
92 <param name="input" format="fasta" type="data" label="Proteins fasta file"/> 93 <param name="input" format="fasta" type="data" label="Proteins fasta file"/>
93 <expand macro="param_scaffold" /> 94 <expand macro="param_scaffold" />
94 <param name="method" type="select" label="Protein clustering method"> 95 <expand macro="param_method" />
95 <option value="gfam" selected="true">GFam</option>
96 <option value="orthofinder">OrthoFinder</option>
97 <option value="orthomcl">OrthoMCL</option>
98 </param>
99 <conditional name="save_hmmscan_log_cond"> 96 <conditional name="save_hmmscan_log_cond">
100 <param name="classifier" type="select" label="Protein classifier"> 97 <param name="classifier" type="select" label="Protein classifier">
101 <option value="blastp" selected="true">blastp</option> 98 <option value="blastp" selected="true">blastp</option>
102 <option value="hmmscan">hmmscan</option> 99 <option value="hmmscan">hmmscan</option>
103 <option value="both">Both blastp and hmmscan</option> 100 <option value="both">Both blastp and hmmscan</option>