Mercurial > repos > rdvelazquez > hyphy_fade

comparison hyphy_fade.xml @ 6:e445c2dc2cce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
author rdvelazquez
date Tue, 20 Nov 2018 12:18:32 -0500
parents f2ee2e0bde56
children a7305e34418f
comparison
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5:f2ee2e0bde56 6:e445c2dc2cce
7 </macros> 7 </macros>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <version_command>HYPHYMP --version | tail -n 1 | awk '{print 9 <version_command>HYPHYMP --version | tail -n 1 | awk '{print
10 $1}'</version_command> 10 $1}'</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$input_file' fade_input.fa && 12 #if $posteriorEstimationMethod == 3:
13 ln -s '$input_nhx' fade_input.nhx && 13 ln -s '$input_file' fade_input.fa &&
14 echo `pwd`/fade_input.fa >> tool_params && 14 ln -s '$input_nhx' fade_input.nhx &&
15 echo `pwd`/fade_input.nhx >> tool_params && 15 echo `pwd`/fade_input.fa >> tool_params &&
16 echo '$branches' >> tool_params && 16 echo `pwd`/fade_input.nhx >> tool_params &&
17 echo '$grid_points' >> tool_params && 17 echo '$branches' >> tool_params &&
18 echo '$substitutionmodel' >> tool_params && 18 echo '$grid_points' >> tool_params &&
19 echo '$posteriorEstimationMethod' >> tool_params && 19 echo '$substitutionmodel' >> tool_params &&
20 echo '$mcmc' >> tool_params && 20 echo '$posteriorEstimationMethod' >> tool_params &&
21 echo '$chain_length' >> tool_params && 21 echo '$concentration' >> tool_params &&
22 echo '$samples' >> tool_params && 22 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
23 echo '$samples_per_chain' >> tool_params && 23 #else:
24 echo '$concentration' >> tool_params && 24 ln -s '$input_file' fade_input.fa &&
25 echo '$branches' >> tool_params && 25 ln -s '$input_nhx' fade_input.nhx &&
26 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log' 26 echo `pwd`/fade_input.fa >> tool_params &&
27 echo `pwd`/fade_input.nhx >> tool_params &&
28 echo '$branches' >> tool_params &&
29 echo '$grid_points' >> tool_params &&
30 echo '$substitutionmodel' >> tool_params &&
31 echo '$posteriorEstimationMethod' >> tool_params &&
32 echo '$mcmc' >> tool_params &&
33 echo '$chain_length' >> tool_params &&
34 echo '$samples' >> tool_params &&
35 echo '$samples_per_chain' >> tool_params &&
36 echo '$concentration' >> tool_params &&
37 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
38 #end if
27 ]]></command> 39 ]]></command>
28 <inputs> 40 <inputs>
29 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 41 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
30 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> 42 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
31 <param name="branches" type="select" label="Set of branches to test"> 43 <param name="branches" type="select" label="Set of branches to test">