Mercurial > repos > rdvelazquez > hyphy_busted

comparison hyphy_busted.xml @ 2:0d4341fca959 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 14:14:48 -0500
parents acaa45acbf91
children f8abbbc7e29e
comparison
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1:8686dd081ecf 2:0d4341fca959
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0">
3 <description>: Branch-site Unrestricted Statistical Test for Episodic Diversification</description> 3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> 8 <expand macro="version_command" />
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 ln -s '$input_file' busted_input.fa && 11 ln -s '$input_file' busted_input.fa &&
12 ln -s '$input_nhx' busted_input.nhx && 12 ln -s '$input_nhx' busted_input.nhx &&
13 echo $gencodeid > tool_params && 13 echo $gencodeid > tool_params &&
16 echo '$branches' >> tool_params && 16 echo '$branches' >> tool_params &&
17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf > '$busted_log' 17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf > '$busted_log'
18 ]]> 18 ]]>
19 </command> 19 </command>
20 <inputs> 20 <inputs>
21 <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> 21 <expand macro="inputs" />
22 <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> 22 <expand macro="gencode" />
23 <param name="gencodeid" type="select" label="Genetic code"> 23 <expand macro="branches" />
24 <option value="1">Universal code</option>
25 <option value="2">Vertebrate mitochondrial DNA code</option>
26 <option value="3">Yeast mitochondrial DNA code</option>
27 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
28 <option value="5">Invertebrate mitochondrial DNA code</option>
29 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
30 <option value="7">Echinoderm mitochondrial DNA code</option>
31 <option value="8">Euplotid Nuclear code</option>
32 <option value="9">Alternative Yeast Nuclear code</option>
33 <option value="10">Ascidian mitochondrial DNA code</option>
34 <option value="11">Flatworm mitochondrial DNA code</option>
35 <option value="12">Blepharisma Nuclear code</option>
36 </param>
37 <param name="branches" type="select" label="Set of branches to test">
38 <option value="1">All branches</option>
39 <option value="2">Internal branches</option>
40 <option value="3">Leaf branches</option>
41 <option value="4">Unlabeled branches</option>
42 </param>
43 </inputs> 24 </inputs>
44 <outputs> 25 <outputs>
45 <data name="busted_log" format="txt" /> 26 <data name="busted_log" format="txt" />
46 <data name="busted_output" format="json" from_work_dir="busted_input.fa.BUSTED.json" /> 27 <data name="busted_output" format="hyphy_json_results" from_work_dir="busted_input.fa.BUSTED.json" />
47 </outputs> 28 </outputs>
48 <tests> 29 <tests>
49 <test> 30 <test>
50 <param name="input_file" ftype="fasta" value="absrel-in1.fa" /> 31 <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" /> 32 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />