Mercurial > repos > greg > gene_family_integrator

comparison macros.xml @ 15:31042dc87180 draft

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Uploaded
author greg
date Fri, 05 May 2017 09:33:20 -0400
parents 2457321db163
children 80996fca62c8
comparison
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14:0dd84595cf37 15:31042dc87180
24 <xml name="requirements_kaks_analysis"> 24 <xml name="requirements_kaks_analysis">
25 <requirements> 25 <requirements>
26 <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement> 26 <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
27 </requirements> 27 </requirements>
28 </xml> 28 </xml>
29 <xml name="requirements_ks_distribution">
30 <requirements>
31 <requirement type="package" version="1.3.0">r-optparse</requirement>
32 </requirements>
33 </xml>
29 <xml name="requirements_gene_family_phylogeny_builder"> 34 <xml name="requirements_gene_family_phylogeny_builder">
30 <requirements> 35 <requirements>
31 <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement> 36 <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
32 </requirements> 37 </requirements>
33 </xml> 38 </xml>
34 <xml name="stdio">
35 <stdio>
36 <exit_code range="1:"/>
37 <exit_code range=":-1"/>
38 <regex match="Error:"/>
39 <regex match="Exception:"/>
40 </stdio>
41 </xml>
42 <xml name="param_codon_alignments"> 39 <xml name="param_codon_alignments">
43 <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments"> 40 <param name="codon_alignments" type="select" label="Codon alignments">
44 <option value="yes" selected="true">Yes</option> 41 <option value="yes" selected="true">Yes</option>
45 <option value="no">No</option> 42 <option value="no">No</option>
46 </param> 43 </param>
47 </xml> 44 </xml>
48 <xml name="param_method"> 45 <xml name="param_method">
82 <option value="mafft" selected="true">MAFFT</option> 79 <option value="mafft" selected="true">MAFFT</option>
83 <option value="pasta">PASTA</option> 80 <option value="pasta">PASTA</option>
84 </param> 81 </param>
85 <when value="mafft" /> 82 <when value="mafft" />
86 <when value="pasta"> 83 <when value="pasta">
87 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" /> 84 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
88 </when> 85 </when>
89 </conditional> 86 </conditional>
90 </xml> 87 </xml>
91 <xml name="cond_remove_gappy_sequences"> 88 <xml name="cond_remove_gappy_sequences">
92 <conditional name="remove_gappy_sequences_cond"> 89 <conditional name="remove_gappy_sequences_cond">