Mercurial > repos > rdvelazquez > hyphy_fade

comparison hyphy_fade.xml @ 9:4377e155b9d1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
author rdvelazquez
date Fri, 07 Jun 2019 10:18:47 -0400
parents a7305e34418f
children
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8:070a1988e661 9:4377e155b9d1
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="2.5.0+galaxy0">
3 <description>: FUBAR* Approach to Directional Evolution (*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
10 $1}'</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
12 #if $posteriorEstimationMethod == 3: 10 ln -s '$input_file' fade_input.fa &&
13 ln -s '$input_file' fade_input.fa && 11 ln -s '$input_nhx' fade_input.nhx &&
14 ln -s '$input_nhx' fade_input.nhx && 12 @HYPHY_INVOCATIN@ fade
15 echo `pwd`/fade_input.fa >> tool_params && 13 --alignment `pwd`/fade_input.fa
16 echo `pwd`/fade_input.nhx >> tool_params && 14 --tree `pwd`/fade_input.nhx
17 echo '$branches' >> tool_params && 15 --branches '$branches'
18 echo '$grid_points' >> tool_params && 16 --model '$substitutionmodel'
19 echo '$substitutionmodel' >> tool_params && 17 --method '$posteriorEstimationMethod'
20 echo '$posteriorEstimationMethod' >> tool_params && 18 --grid '$grid_points'
21 echo '$concentration' >> tool_params && 19 --concentration_parameter '$concentration'
22 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log' 20 --chains '$mcmc'
23 #else: 21 --chain-length '$chain_length'
24 ln -s '$input_file' fade_input.fa && 22 --burn-in '$samples'
25 ln -s '$input_nhx' fade_input.nhx && 23 --samples '$samples_per_chain'
26 echo `pwd`/fade_input.fa >> tool_params && 24 > '$fade_log'
27 echo `pwd`/fade_input.nhx >> tool_params &&
28 echo '$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
39 ]]></command> 25 ]]></command>
40 <inputs> 26 <inputs>
41 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/> 27 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
42 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/> 28 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
43 <param name="branches" type="select" label="Set of branches to test"> 29 <param name="branches" type="select" label="Set of branches to test">