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comparison hyphy_meme.xml @ 3:f84a42d3ef98 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 10:20:49 -0400
parents cffd8bd6e3ec
children
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2:15591ab0d53a 3:f84a42d3ef98
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_meme" name="HyPhy-MEME" version="2.5.0+galaxy0">
3 <description>: Mixed Effects Model of Evolution</description> 3 <description>: Mixed Effects Model of Evolution</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 export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} && 10 ln -s '$input_file' meme_input.fa &&
12 ln -s '$input_file' meme_input.fa && 11 ln -s '$input_nhx' meme_input.nhx &&
13 ln -s '$input_nhx' meme_input.nhx && 12 @HYPHY_INVOCATION@ meme
14 echo $gencodeid > tool_params && 13 --alignment `pwd`/meme_input.fa
15 echo `pwd`/meme_input.fa >> tool_params && 14 --tree `pwd`/meme_input.nhx
16 echo `pwd`/meme_input.nhx >> tool_params && 15 --code '$gencodeid'
17 echo $branches >> tool_params && 16 --branches '$branches'
18 echo $p_value >> tool_params && 17 --pvalue '$p_value'
19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log' 18 > '$meme_log'
20 ]]> 19 ]]>
21 </command> 20 </command>
22 <inputs> 21 <inputs>
23 <expand macro="inputs" /> 22 <expand macro="inputs" />
24 <expand macro="gencode" /> 23 <expand macro="gencode" />