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comparison raxml.xml @ 3:14eb2acf30e3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 7e554792519972b5988f8e451d7466a62cbbc626"
author iuc
date Sun, 15 Mar 2020 15:35:33 -0400
parents a4b71be30c3c
children 73a469f7dc96
comparison
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2:a4b71be30c3c 3:14eb2acf30e3
1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy1"> 1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy2">
2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description> 2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="8.2.4">raxml</requirement> 4 <requirement type="package" version="8.2.4">raxml</requirement>
5 <requirement type="package" version="3.6">python</requirement> 5 <requirement type="package" version="3.6">python</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1 8 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
9 #set $slots = $getVar('GALAXY_SLOTS', 1) 9 slots=\${GALAXY_SLOTS:-1};
10 #if $slots == 1: 10 if [ "\$slots" == "1" ]; then
11 raxmlHPC 11 bin="raxmlHPC";
12 ## Cannot have -T 1 12 else
13 #else: 13 bin="raxmlHPC-PTHREADS -T \$slots";
14 raxmlHPC-PTHREADS 14 fi;
15 -T $slots 15 \$bin
16 #end if
17 -s '$infile' 16 -s '$infile'
18 -n galaxy 17 -n galaxy
19 #if $search_model_selector.model_type == 'aminoacid': 18 #if $search_model_selector.model_type == 'aminoacid':
20 -m ${search_model_selector.base_model}${search_model_selector.aa_search_matrix}${search_model_selector.aa_model_empirical_base_frequencies} 19 -m ${search_model_selector.base_model}${search_model_selector.aa_search_matrix}${search_model_selector.aa_model_empirical_base_frequencies}
21 #else: 20 #else: