Mercurial > repos > iuc > hyphy_meme

comparison hyphy_meme.xml @ 32:5d8389d684bf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:22:00 +0000
parents cdbb233119cb
children 5fd8dc04d6af
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31:cdbb233119cb 32:5d8389d684bf
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@TOOL_VERSION@+galaxy2" profile="19.09"> 2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@TOOL_VERSION@+galaxy2" profile="19.09">
3 <description>Mixed Effects Model of Evolution</description> 3 <description>Mixed Effects Model of Evolution</description>
4 <expand macro="bio_tools"/>
5 <macros> 4 <macros>
6 <import>macros.xml</import> 5 <import>macros.xml</import>
7 </macros> 6 </macros>
7 <expand macro="bio_tools"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @SYMLINK_FILES@ 10 @SYMLINK_FILES@
11 @HYPHYMPI@ meme 11 @HYPHYMPI@ meme
12 --alignment ./$input_file 12 --alignment ./$input_file
13 @INPUT_TREE@ 13 @INPUT_TREE@
14 --code '$gencodeid' 14 --code '$gencodeid'
15 @branch_options@ 15 @branch_options@
16 --pvalue '$p_value' 16 --pvalue '$p_value'
17 --resample $resample
17 --output '$meme_output' 18 --output '$meme_output'
18 --full-model '$full_model' 19 --full-model '$full_model'
19 @ERRORS@ 20 @ERRORS@
20 ]]></command> 21 ]]></command>
21 <inputs> 22 <inputs>
22 <expand macro="inputs"/> 23 <expand macro="inputs"/>
23 <expand macro="gencode"/> 24 <expand macro="gencode"/>
24 <expand macro="branches"/> 25 <expand macro="branches"/>
25 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> 26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
27 <expand macro="resample"/>
26 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" /> 28 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" />
27 </inputs> 29 </inputs>
28 <outputs> 30 <outputs>
29 <data name="meme_output" format="hyphy_results.json" /> 31 <data name="meme_output" format="hyphy_results.json" />
30 </outputs> 32 </outputs>