Mercurial > repos > rdvelazquez > hyphy_busted

comparison hyphy_busted.xml @ 4:f8abbbc7e29e 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 10:18:17 -0400
parents 0d4341fca959
children
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3:d0a3511a8f33 4:f8abbbc7e29e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="2.5.0+galaxy0">
3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description> 3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</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 <expand macro="version_command" />
9 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
10 <![CDATA[ 9 <![CDATA[
11 ln -s '$input_file' busted_input.fa && 10 ln -s '$input_file' busted_input.fa &&
12 ln -s '$input_nhx' busted_input.nhx && 11 ln -s '$input_nhx' busted_input.nhx &&
13 echo $gencodeid > tool_params && 12 @HYPHY_INVOCATION@ busted
14 echo `pwd`/busted_input.fa >> tool_params && 13 --alignment `pwd`/busted_input.fa
15 echo `pwd`/busted_input.nhx >> tool_params && 14 --tree `pwd`/busted_input.nhx
16 echo '$branches' >> tool_params && 15 --code $gencodeid
17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf > '$busted_log' 16 --branches '$branches'
17 > '$busted_log'
18 ]]> 18 ]]>
19 </command> 19 </command>
20 <inputs> 20 <inputs>
21 <expand macro="inputs" /> 21 <expand macro="inputs" />
22 <expand macro="gencode" /> 22 <expand macro="gencode" />