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comparison hyphy_meme.xml @ 2:b15d64d85c03 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 16:46:45 -0500
parents d02c8e6f7f2a
children 33040ebb30c6
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1:d02c8e6f7f2a 2:b15d64d85c03
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="@VERSION@+galaxy1">
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 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' meme_input.fa && 9 ln -s '$input_file' meme_input.fa &&
10 ln -s '$input_nhx' meme_input.nhx && 10 ln -s '$input_nhx' meme_input.nhx &&
11 @HYPHY_INVOCATION@ meme 11 @HYPHYMPI@ meme
12 --alignment ./meme_input.fa 12 --alignment ./meme_input.fa
13 --tree ./meme_input.nhx 13 --tree ./meme_input.nhx
14 --code '$gencodeid' 14 --code '$gencodeid'
15 --branches '$branches' 15 --branches '$branches'
16 --pvalue '$p_value' 16 --pvalue '$p_value'
17 --output '$meme_output'
17 > '$meme_log' 18 > '$meme_log'
18 ]]></command> 19 ]]></command>
19 <inputs> 20 <inputs>
20 <expand macro="inputs"/> 21 <expand macro="inputs"/>
21 <expand macro="gencode"/> 22 <expand macro="gencode"/>
22 <expand macro="branches"/> 23 <expand macro="branches"/>
23 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> 24 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
24 </inputs> 25 </inputs>
25 <outputs> 26 <outputs>
26 <data name="meme_log" format="txt"/> 27 <data name="meme_log" format="txt"/>
27 <data name="meme_output" format="hyphy_results.json" from_work_dir="meme_input.fa.MEME.json"/> 28 <data name="meme_output" format="hyphy_results.json" />
28 </outputs> 29 </outputs>
29 <tests> 30 <tests>
30 <test> 31 <test>
31 <param name="input_file" ftype="fasta" value="meme-in1.fa"/> 32 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
32 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/> 33 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>