Mercurial > repos > iuc > hyphy_slac

comparison hyphy_slac.xml @ 3:242ed2357a01 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 16:47:07 -0500
parents a603e2f909e5
children 8522e7cc4fb4
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2:a603e2f909e5 3:242ed2357a01
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1">
3 <description>Single Likelihood Ancestor Counting</description> 3 <description>Single Likelihood Ancestor Counting</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 '$input_file' slac_input.fa && 9 ln -s '$input_file' slac_input.fa &&
10 ln -s '$input_nhx' slac_input.nhx && 10 ln -s '$input_nhx' slac_input.nhx &&
11 @HYPHY_INVOCATION@ slac 11 hyphy slac
12 --alignment ./slac_input.fa 12 --alignment ./slac_input.fa
13 --tree ./slac_input.nhx 13 --tree ./slac_input.nhx
14 --code '$gencodeid' 14 --code '$gencodeid'
15 --branches '$branches' 15 --branches '$branches'
16 --samples '$number_of_samples' 16 --samples '$number_of_samples'
17 --pvalue '$p_value' 17 --pvalue '$p_value'
18 --output '$slac_output'
18 > '$slac_log' 19 > '$slac_log'
19 ]]></command> 20 ]]></command>
20 <inputs> 21 <inputs>
21 <expand macro="inputs"/> 22 <expand macro="inputs"/>
22 <expand macro="gencode"/> 23 <expand macro="gencode"/>
24 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> 25 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
25 <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/> 26 <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
26 </inputs> 27 </inputs>
27 <outputs> 28 <outputs>
28 <data name="slac_log" format="txt"/> 29 <data name="slac_log" format="txt"/>
29 <data name="slac_output" format="hyphy_results.json" from_work_dir="slac_input.fa.SLAC.json"/> 30 <data name="slac_output" format="hyphy_results.json" />
30 </outputs> 31 </outputs>
31 <tests> 32 <tests>
32 <test> 33 <test>
33 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> 34 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
34 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 35 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>