Mercurial > repos > iuc > raxml
comparison raxml.xml @ 3:14eb2acf30e3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 7e554792519972b5988f8e451d7466a62cbbc626"
author | iuc |
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date | Sun, 15 Mar 2020 15:35:33 -0400 |
parents | a4b71be30c3c |
children | 73a469f7dc96 |
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2:a4b71be30c3c | 3:14eb2acf30e3 |
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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: |