Mercurial > repos > rdvelazquez > hyphy_absrel

comparison hyphy_absrel.xml @ 13:35c1c523ae44 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 10:17:13 -0400
parents edf8263a39cb
children
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12:adfc44cee2b5 13:35c1c523ae44
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="2.5.0+galaxy0">
3 <description>adaptive Branch Site Random Effects Likelihood</description> 3 <description>absrel</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 '$input_file' absrel_input.fa && 10 ln -s '$input_file' absrel_input.fa &&
12 ln -s '$input_nhx' absrel_input.nhx && 11 ln -s '$input_nhx' absrel_input.nhx &&
13 echo $gencodeid > tool_params && 12 @HYPHY_INVOCATION@ absrel
14 echo `pwd`/absrel_input.fa >> tool_params && 13 --alignment `pwd`/absrel_input.fa
15 echo `pwd`/absrel_input.nhx >> tool_params && 14 --tree `pwd/absrel_input.nhx
16 echo '$branches' >> tool_params && 15 --code '$gencodeid'
17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf 16 --branches '$branches'
18 #if $log:
19 > '$absrel_log' 17 > '$absrel_log'
20 #end if
21 ]]> 18 ]]>
22 </command> 19 </command>
23 <inputs> 20 <inputs>
24 <expand macro="inputs" /> 21 <expand macro="inputs" />
25 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" /> 22 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" />