Mercurial > repos > iuc > hyphy_gard

comparison hyphy_gard.xml @ 23:a0731e81e0c2 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 10:25:18 +0000
parents 42efcb0955e6
children 1fb98a84e86d
comparison
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22:3b96e92e8ec3 23:a0731e81e0c2
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0" profile="19.09"> 2 <tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0" profile="19.09">
3 <description>Genetic Algorithm for Recombination Detection</description> 3 <description>Genetic Algorithm for Recombination Detection</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@OPERATION@">GARD</token>
7 <token name="@operation@">gard</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 '$input_file' gard_input.fa && 11 ln -s '$input_file' input.$input_file.extension &&
12 #set $input_file = 'input.%s' % $input_file.extension
10 @HYPHYMPI@ gard 13 @HYPHYMPI@ gard
11 --alignment ./gard_input.fa 14 --alignment ./$input_file
12 --type '$datatype.value' 15 --type '$datatype.value'
13 #if str($datatype.value) == 'codon': 16 #if str($datatype.value) == 'codon':
14 --code '$datatype.gencodeid' 17 --code '$datatype.gencodeid'
15 #elif str($datatype.value) == 'amino-acid': 18 #elif str($datatype.value) == 'amino-acid':
16 --model '$datatype.model' 19 --model '$datatype.model'
21 #end if 24 #end if
22 --output '$translated' 25 --output '$translated'
23 --output-lf '$gard_output' 26 --output-lf '$gard_output'
24 > '$gard_log' 27 > '$gard_log'
25 ; 28 ;
26 @CATCH_MPIERR@ 29 @CATCH_ERROR@
27 ]]></command> 30 ]]></command>
28 <inputs> 31 <inputs>
29 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 32 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" />
30 <conditional name="datatype"> 33 <conditional name="datatype">
31 <param argument="--type" name="value" type="select" label="Alignment kind"> 34 <param argument="--type" name="value" type="select" label="Alignment kind">
32 <option value="nucleotide">Nucleotide</option> 35 <option value="nucleotide">Nucleotide</option>
33 <option value="amino-acid">Amino acid</option> 36 <option value="amino-acid">Amino acid</option>
34 <option value="codon">Codon</option> 37 <option value="codon">Codon</option>
62 <data name="translated" format="hyphy_results.json" /> 65 <data name="translated" format="hyphy_results.json" />
63 </outputs> 66 </outputs>
64 <tests> 67 <tests>
65 <test> 68 <test>
66 <param name="input_file" ftype="fasta" value="gard-in1.fa"/> 69 <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
67 <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/> 70 <output name="gard_output" file="gard-out1.nex" compare="sim_size"/>
68 </test> 71 </test>
69 </tests> 72 </tests>
70 <help><![CDATA[ 73 <help><![CDATA[
71 74
72 GARD : Genetic Algorithms for Recombination Detection. 75 GARD : Genetic Algorithms for Recombination Detection.