Mercurial > repos > iuc > hyphy_meme

comparison hyphy_meme.xml @ 23:2f07f5b4e47b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:24:10 +0000
parents 5b380f4dbf1c
children e0763df98352
comparison
equal deleted inserted replaced
22:24a21a467399 23:2f07f5b4e47b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0" profile="19.09"> 2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1" profile="19.09">
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 <token name="@OPERATION@">MEME</token>
7 <token name="@operation@">meme</token>
6 </macros> 8 </macros>
7 <expand macro="requirements"/> 9 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' meme_input.fa && 11 @SYMLINK_FILES@
10 ln -s '$input_nhx' meme_input.nhx &&
11 @HYPHYMPI@ meme 12 @HYPHYMPI@ meme
12 --alignment ./meme_input.fa 13 --alignment ./$input_file
13 --tree ./meme_input.nhx 14 #if $input_nhx:
15 --tree ./input.nhx
16 #end if
14 --code '$gencodeid' 17 --code '$gencodeid'
15 --branches '$branches' 18 --branches '$branches'
16 --pvalue '$p_value' 19 --pvalue '$p_value'
17 --output '$meme_output' 20 --output '$meme_output'
21 --full-model '$full_model'
18 > '$meme_log' 22 > '$meme_log'
19 ; 23 ;
20 @CATCH_MPIERR@ 24 @CATCH_ERROR@
21 ]]></command> 25 ]]></command>
22 <inputs> 26 <inputs>
23 <expand macro="inputs"/> 27 <expand macro="inputs"/>
24 <expand macro="gencode"/> 28 <expand macro="gencode"/>
25 <expand macro="branches"/> 29 <expand macro="branches"/>
26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> 30 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
31 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" />
27 </inputs> 32 </inputs>
28 <outputs> 33 <outputs>
29 <data name="meme_log" format="txt"/> 34 <data name="meme_log" format="txt"/>
30 <data name="meme_output" format="hyphy_results.json" /> 35 <data name="meme_output" format="hyphy_results.json" />
31 </outputs> 36 </outputs>