Mercurial > repos > iuc > hyphy_meme

comparison hyphy_meme.xml @ 25:e0763df98352 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 17:59:28 +0000
parents 2f07f5b4e47b
children 45a2366d777e
comparison
equal deleted inserted replaced
24:efdd06f7f857 25:e0763df98352
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1" profile="19.09"> 2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy2" 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>
8 </macros> 6 </macros>
9 <expand macro="requirements"/> 7 <expand macro="requirements"/>
10 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
11 @SYMLINK_FILES@ 9 @SYMLINK_FILES@
12 @HYPHYMPI@ meme 10 @HYPHYMPI@ meme
13 --alignment ./$input_file 11 --alignment ./$input_file
14 #if $input_nhx: 12 @INPUT_TREE@
15 --tree ./input.nhx
16 #end if
17 --code '$gencodeid' 13 --code '$gencodeid'
18 --branches '$branches' 14 @branch_options@
19 --pvalue '$p_value' 15 --pvalue '$p_value'
20 --output '$meme_output' 16 --output '$meme_output'
21 --full-model '$full_model' 17 --full-model '$full_model'
22 > '$meme_log' 18 @ERRORS@
23 ;
24 @CATCH_ERROR@
25 ]]></command> 19 ]]></command>
26 <inputs> 20 <inputs>
27 <expand macro="inputs"/> 21 <expand macro="inputs"/>
28 <expand macro="gencode"/> 22 <expand macro="gencode"/>
29 <expand macro="branches"/> 23 <expand macro="branches"/>
30 <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"/>
31 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" /> 25 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" />
32 </inputs> 26 </inputs>
33 <outputs> 27 <outputs>
34 <data name="meme_log" format="txt"/>
35 <data name="meme_output" format="hyphy_results.json" /> 28 <data name="meme_output" format="hyphy_results.json" />
36 </outputs> 29 </outputs>
37 <tests> 30 <tests>
38 <test> 31 <test>
39 <param name="input_file" ftype="fasta" value="meme-in1.fa"/> 32 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>