Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 51:9962341547d3 draft

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author greg
date Thu, 05 Oct 2017 14:23:17 -0400
parents 4c9a4aa6adce
children 3adaaeb651c0
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50:4c9a4aa6adce 51:9962341547d3
1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.3.0"> 1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.3.0">
2 <description>builds phylogenetic trees of aligned orthologous gene family clusters</description> 2 <description>builds phylogenetic trees of aligned orthologous gene family clusters</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_gene_family_phylogeny_builder" /> 6 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_gene_family_phylogeny_builder</requirement>
8 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 #set input_dir = 'input_dir' 10 #set input_dir = 'input_dir'
9 #set tree_inference = $tree_inference_cond.tree_inference 11 #set tree_inference = $tree_inference_cond.tree_inference
10 #if str($tree_inference) == 'raxml': 12 #if str($tree_inference) == 'raxml':
11 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 13 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
16 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates 18 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
17 #end if 19 #end if
18 mkdir $input_dir && 20 mkdir $input_dir &&
19 #for $i in $input: 21 #for $i in $input:
20 #set filename = $i.file_name 22 #set filename = $i.file_name
21 #set name =$i.name 23 #set name = $i.name
22 ln -s $filename $input_dir/$name && 24 ln -s $filename $input_dir/$name &&
23 #end for 25 #end for
24 GeneFamilyPhylogenyBuilder 26 GeneFamilyPhylogenyBuilder
25 --orthogroup_aln '$input_dir' 27 --orthogroup_aln '$input_dir'
26 --scaffold '$scaffold.fields.path' 28 --scaffold '$scaffold.fields.path'