Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 70:850363a7e1ae draft

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Uploaded
author greg
date Fri, 17 Feb 2017 11:29:40 -0500
parents 0d689b9662ec
children c443ffe51d49
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69:0d689b9662ec 70:850363a7e1ae
1 <tool id="plant_tribes_gene_family_classifier" name="Classify gene sequences" version="0.3"> 1 <tool id="plant_tribes_gene_family_classifier" name="Classify gene sequences" version="0.6.0">
2 <description>into precomputed orthologous gene family clusters</description> 2 <description>into precomputed orthologous gene family clusters</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.3">plant_tribes_gene_family_classifier</requirement> 4 <requirement type="package" version="0.6">plant_tribes_gene_family_classifier</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <!-- Anything other than zero is an error --> 7 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 <exit_code range=":-1" /> 9 <exit_code range=":-1" />
79 #if specify_super_orthos: 79 #if specify_super_orthos:
80 --super_orthogroups $super_orthogroups 80 --super_orthogroups $super_orthogroups
81 #end if 81 #end if
82 #if $single_copy_orthogroup: 82 #if $single_copy_orthogroup:
83 #if str($single_copy) == 'custom': 83 #if str($single_copy) == 'custom':
84 --single_copy_custom 84 #set single_copy_custom_cond = $single_copy_cond.single_copy_custom_cond
85 #set single_copy_custom = $single_copy_custom_cond.single_copy_custom
86 #if str($single_copy_custom) == 'no':
87 #set single_copy_custom_config = $os.path.join($scaffold.fields.path, 'singleCopy.config')
88 --single_copy_custom '$single_copy_custom_config'
89 #else:
90 --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config'
91 #end if
85 #else: 92 #else:
86 --single_copy_taxa $single_copy_cond.single_copy_taxa 93 --single_copy_taxa $single_copy_cond.single_copy_taxa
87 --taxa_present $single_copy_cond.taxa_present 94 --taxa_present $single_copy_cond.taxa_present
88 #end if 95 #end if
89 #end if 96 #end if
185 <conditional name="single_copy_cond"> 192 <conditional name="single_copy_cond">
186 <param name="single_copy" type="select" label="Select single copy configuration"> 193 <param name="single_copy" type="select" label="Select single copy configuration">
187 <option value="custom" selected="true">Single copy orthogroup custom configuration</option> 194 <option value="custom" selected="true">Single copy orthogroup custom configuration</option>
188 <option value="taxa">Minimum single copy taxa required in orthogroup</option> 195 <option value="taxa">Minimum single copy taxa required in orthogroup</option>
189 </param> 196 </param>
190 <when value="custom"/> 197 <when value="custom">
198 <conditional name="single_copy_custom_cond">
199 <param name="single_copy_custom" type="select" label="Select single copy orthogroup custom configuration?" help="Select No to use the default configuration">
200 <option value="no" selected="true">No</option>
201 <option value="yes">Yes</option>
202 </param>
203 <when value="no"/>
204 <when value="yes">
205 <param name="single_copy_custom_config" format="txt" type="data" label="Select single copy custom configuration file"/>
206 </when>
207 </conditional>
208 </when>
191 <when value="taxa"> 209 <when value="taxa">
192 <param name="single_copy_taxa" type="integer" value="20" label="Minimum single copy taxa required in orthogroup"/> 210 <param name="single_copy_taxa" type="integer" value="20" label="Minimum single copy taxa required in orthogroup"/>
193 <param name="taxa_present" type="integer" value="21" label="Minimum taxa required in single copy orthogroup"/> 211 <param name="taxa_present" type="integer" value="21" label="Minimum taxa required in single copy orthogroup"/>
194 </when> 212 </when>
195 </conditional> 213 </conditional>