Mercurial > repos > iuc > hyphy_fade

comparison hyphy_fade.xml @ 2:f65e8fe7d5b8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:46:01 -0500
parents da4192d32e10
children b959fd359a6b
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1:da4192d32e10 2:f65e8fe7d5b8
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@+galaxy1">
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 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$input_file' fade_input.fa && 10 ln -s '$input_file' fade_input.fa &&
11 ln -s '$input_nhx' fade_input.nhx && 11 ln -s '$input_nhx' fade_input.nhx &&
12 @HYPHY_INVOCATION@ fade 12 hyphy fade
13 --alignment ./fade_input.fa 13 --alignment ./fade_input.fa
14 --tree ./fade_input.nhx 14 --tree ./fade_input.nhx
15 --branches '$branches' 15 --branches '$branches'
16 --model '$model' 16 --model '$model'
17 --method '$posteriorEstimationMethod' 17 --method '$posteriorEstimationMethod'
21 --chains '$mcmc' 21 --chains '$mcmc'
22 --chain-length '$chain_length' 22 --chain-length '$chain_length'
23 --burn-in '$samples' 23 --burn-in '$samples'
24 --samples '$samples_per_chain' 24 --samples '$samples_per_chain'
25 #end if 25 #end if
26 --output '$fade_output'
26 > '$fade_log' 27 > '$fade_log'
27 ]]></command> 28 ]]></command>
28 <inputs> 29 <inputs>
29 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/> 30 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
30 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/> 31 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
47 Bayes approximations (fastest, recommended default)</option> 48 Bayes approximations (fastest, recommended default)</option>
48 </param> 49 </param>
49 </inputs> 50 </inputs>
50 <outputs> 51 <outputs>
51 <data name="fade_log" format="txt"/> 52 <data name="fade_log" format="txt"/>
52 <data name="fade_output" format="hyphy_results.json" from_work_dir="fade_input.fa.FADE.json"/> 53 <data name="fade_output" format="hyphy_results.json" />
53 </outputs> 54 </outputs>
54 <tests> 55 <tests>
55 <test> 56 <test>
56 <param name="input_file" ftype="fasta" value="fade-in1.fa"/> 57 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
57 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/> 58 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>