Mercurial > repos > iuc > hyphy_fubar

comparison hyphy_fubar.xml @ 3:b73b35db4664 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:45:00 -0500
parents 6943fbec145c
children 93a0cf4ea5fc
comparison
equal deleted inserted replaced
2:6943fbec145c 3:b73b35db4664
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy1">
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 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' fubar_input.fa && 9 ln -s '$input_file' fubar_input.fa &&
10 ln -s '$input_nhx' fubar_input.nhx && 10 ln -s '$input_nhx' fubar_input.nhx &&
11 @HYPHY_INVOCATION@ fubar 11 hyphy fubar
12 --alignment ./fubar_input.fa 12 --alignment ./fubar_input.fa
13 --tree ./fubar_input.nhx 13 --tree ./fubar_input.nhx
14 --code '$gencodeid' 14 --code '$gencodeid'
15 --method '$posterior' 15 --method '$posterior'
16 --grid '$grid_points' 16 --grid '$grid_points'
36 <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/> 36 <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/>
37 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/> 37 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
38 </inputs> 38 </inputs>
39 <outputs> 39 <outputs>
40 <data name="fubar_log" format="txt"/> 40 <data name="fubar_log" format="txt"/>
41 <data name="fubar_output" format="hyphy_results.json" from_work_dir="fubar_input.fa.FUBAR.json"/> 41 <data name="fubar_output" format="hyphy_results.json" from_work_dir="fubar_input.fa.FUBAR.json" />
42 </outputs> 42 </outputs>
43 <tests> 43 <tests>
44 <test> 44 <test>
45 <param name="input_file" ftype="fasta" value="fubar-in1.fa"/> 45 <param name="input_file" ftype="fasta" value="fubar-in1.fa"/>
46 <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/> 46 <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/>