Mercurial > repos > rdvelazquez > hyphy_fade

comparison hyphy_fade.xml @ 1:9e5fa270a08a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'bff24ad0eccc4083de076adc029c5c3ac50e2852\n'-dirty
author rdvelazquez
date Sun, 18 Nov 2018 22:57:28 -0500
parents bcd72352534f
children 77bd5890fc28
comparison
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0:bcd72352534f 1:9e5fa270a08a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
3 <description>: FUBAR* Approach to Directional Selection (*Fast 3 <description>: FUBAR* Approach to Directional Evolution (*Fast
4 Unconstrained Bayesian Approximation)</description> 4 Unconstrained Bayesian Approximation)</description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
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 ln -s '$input_file' fade_input.fa &&
13 ln -s '$input_nhx' fade_input.nhx && 13 ln -s '$input_nhx' fade_input.nhx &&
14 echo $substitutionmodel > tool_params &&
15 echo `pwd`/fade_input.fa >> tool_params && 14 echo `pwd`/fade_input.fa >> tool_params &&
16 echo `pwd`/fade_input.nhx >> tool_params && 15 echo `pwd`/fade_input.nhx >> tool_params &&
16 echo '$branches' >> tool_params &&
17 echo '$grid_points' >> tool_params && 17 echo '$grid_points' >> tool_params &&
18 echo $substitutionmodel > tool_params &&
18 echo '$mcmc' >> tool_params && 19 echo '$mcmc' >> tool_params &&
19 echo '$chain_length' >> tool_params && 20 echo '$chain_length' >> tool_params &&
20 echo '$samples' >> tool_params && 21 echo '$samples' >> tool_params &&
21 echo '$samples_per_chain' >> tool_params && 22 echo '$samples_per_chain' >> tool_params &&
22 echo '$concentration' >> tool_params && 23 echo '$concentration' >> tool_params &&
24 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log' 25 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
25 ]]></command> 26 ]]></command>
26 <inputs> 27 <inputs>
27 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 28 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
28 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> 29 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
30 <param name="branches" type="select" label="Set of branches to test">
31 <option value="1">All branches</option>
32 <option value="2">Internal branches</option>
33 <option value="3">Leaf branches</option>
34 <option value="4">Unlabeled branches</option>
35 </param>
29 <param name="substitutionmodel" type="select" label="Substitution Model"> 36 <param name="substitutionmodel" type="select" label="Substitution Model">
30 <option value="1">LG (Generalist empirical model from Le and 37 <option value="1">LG (Generalist empirical model from Le and
31 Gascuel 2008)</option> 38 Gascuel 2008)</option>
32 <option value="2">WAG (Generalist empirical model from Whelon 39 <option value="2">WAG (Generalist empirical model from Whelon
33 and Goldman 2001)</option> 40 and Goldman 2001)</option>
77 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/> 84 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
78 <output name="fade_output" file="fade-out1.json" compare="sim_size"/> 85 <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
79 </test> 86 </test>
80 </tests> 87 </tests>
81 <help><![CDATA[ 88 <help><![CDATA[
82 FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect site evolving under directional evolution in protien alignments. 89 FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect sites evolving under directional evolution in protien alignments.
83 ]]></help> 90 ]]></help>
84 <expand macro="citations"> 91 <expand macro="citations">
85 <citation type="doi">10.1093/molbev/msv022</citation> 92 <citation type="doi">10.1093/molbev/msv022</citation>
86 </expand> 93 </expand>
87 </tool> 94 </tool>