Mercurial > repos > iuc > hyphy_fubar

comparison hyphy_fubar.xml @ 24:c5ef306c2041 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:24:45 +0000
parents 3db56014322f
children cd41e7a4d35f
comparison
equal deleted inserted replaced
23:f9f0518a0053 24:c5ef306c2041
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy0" profile="19.09"> 2 <tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy0" profile="19.09">
3 <description>Fast Unconstrained Bayesian AppRoximation</description> 3 <description>Fast Unconstrained Bayesian AppRoximation</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@OPERATION@">FUBAR</token>
7 <token name="@operation@">fubar</token>
6 </macros> 8 </macros>
7 <expand macro="requirements"/> 9 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' fubar_input.fa && 11 @SYMLINK_FILES@
10 ln -s '$input_nhx' fubar_input.nhx &&
11 hyphy fubar 12 hyphy fubar
12 --alignment ./fubar_input.fa 13 --alignment ./$input_file
13 --tree ./fubar_input.nhx 14 #if $input_nhx:
15 --tree ./input.nhx
16 #end if
14 --code '$gencodeid' 17 --code '$gencodeid'
15 --method '$posteriorEstimationMethod.method' 18 --method '$posteriorEstimationMethod.method'
16 --grid '$grid_points' 19 --grid '$grid_points'
17 @posteriorEstimationMethod_cmd@ 20 @posteriorEstimationMethod_cmd@
18 --concentration_parameter '$concentration' 21 --concentration_parameter '$concentration'
19 > '$fubar_log' 22 > '$fubar_log' ;
23 @CATCH_ERROR@
20 ]]></command> 24 ]]></command>
21 <inputs> 25 <inputs>
22 <expand macro="inputs"/> 26 <expand macro="inputs"/>
23 <expand macro="gencode"/> 27 <expand macro="gencode"/>
24 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" /> 28 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" />
26 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" /> 30 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" />
27 31
28 </inputs> 32 </inputs>
29 <outputs> 33 <outputs>
30 <data name="fubar_log" format="txt"/> 34 <data name="fubar_log" format="txt"/>
31 <data name="fubar_output" format="hyphy_results.json" from_work_dir="fubar_input.fa.FUBAR.json" /> 35 <data name="fubar_output" format="hyphy_results.json" />
32 </outputs> 36 </outputs>
33 <tests> 37 <tests>
34 <test> 38 <test>
35 <param name="input_file" ftype="fasta" value="fubar-in1.fa"/> 39 <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/>
36 <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/> 40 <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/>
37 <param name="posterior" value="Variational-Bayes"/> 41 <param name="posterior" value="Variational-Bayes"/>
38 <output name="fubar_output" file="fubar-out1.json" compare="sim_size"/> 42 <output name="fubar_output" file="fubar-out1.json" compare="sim_size"/>
39 </test> 43 </test>
40 </tests> 44 </tests>