Mercurial > repos > rdvelazquez > hyphy_gard

comparison hyphy_gard.xml @ 5:9640a5b51502 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
author rdvelazquez
date Fri, 07 Jun 2019 10:20:19 -0400
parents 876a69d2c6d7
children
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4:876a69d2c6d7 5:9640a5b51502
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_gard" name="HyPhy-GARD" version="2.5.0+galaxy0">
3 <description>: Recombination Detection</description> 3 <description>: Recombination Detection</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <command detect_errors="exit_code">
8 <requirement type="package" version="1.0.4">translate-gard</requirement> 8 <![CDATA[
9 </expand>
10 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 export MPI_NODE_COUNT=\${GALAXY_SLOTS:-2} &&
13 ln -s '$input_file' gard_input.fa && 9 ln -s '$input_file' gard_input.fa &&
14 echo `pwd`/gard_input.fa > tool_params && 10 @HYPHY_INVOCATION@ gard
15 echo "010010" >> tool_params && 11 --alignment `pwd`/gard_input.fa
16 echo $rate_cond.rate >> tool_params && 12 --type
17 #if str($rate_cond.rate) != "1": 13 --code
18 echo $rate_cond.rate_classes >> tool_params && 14 --model
19 #end if 15 --rv '$rate'
20 echo `pwd`/"gard_input.GARD" >> tool_params && 16 --rate-classes '$rate_classes'
21 @HYPHYMPI_INVOCATION@ \$HYPHYMPI_LIB/TemplateBatchFiles/GARD.bf > '$gard_log' && 17
22 translate-gard -i gard_input.GARD -j gard_input.GARD.json -o gard_input.fa.translated.json 18 > '$gard_log' &&
23 ]]></command> 19 ]]></command>
24 <inputs> 20 <inputs>
25 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 21 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
26 <conditional name="rate_cond"> 22 <conditional name="rate_cond">
27 <param name="rate" type="select" label="Rate variation"> 23 <param name="rate" type="select" label="Rate variation">
28 <option value="1">None</option> 24 <option value="None">None</option>
29 <option value="2">General Discrete</option> 25 <option value="GDD">General Discrete</option>
30 <option value="3">Beta-Gamma</option> 26 <option value="Gamma">Beta-Gamma</option>
31 </param> 27 </param>
32 <when value="1"/> 28 <when value="1"/>
33 <when value="2"> 29 <when value="2">
34 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/> 30 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
35 </when> 31 </when>