Mercurial > repos > rdvelazquez > hyphy_meme

comparison hyphy_meme.xml @ 1:cffd8bd6e3ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'0a555981fa0582d59012c76c01c466db490831ed\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 14:31:06 -0500
parents 1fe6d55b5a9b
children f84a42d3ef98
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0:1fe6d55b5a9b 1:cffd8bd6e3ec
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 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> 8 <expand macro="version_command" />
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} && 11 export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
12 ln -s '$input_file' meme_input.fa && 12 ln -s '$input_file' meme_input.fa &&
13 ln -s '$input_nhx' meme_input.nhx && 13 ln -s '$input_nhx' meme_input.nhx &&
18 echo $p_value >> tool_params && 18 echo $p_value >> tool_params &&
19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log' 19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
20 ]]> 20 ]]>
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> 23 <expand macro="inputs" />
24 <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> 24 <expand macro="gencode" />
25 <param name="gencodeid" type="select" label="Genetic code"> 25 <expand macro="branches" />
26 <option value="1">Universal code</option>
27 <option value="2">Vertebrate mitochondrial DNA code</option>
28 <option value="3">Yeast mitochondrial DNA code</option>
29 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
30 <option value="5">Invertebrate mitochondrial DNA code</option>
31 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
32 <option value="7">Echinoderm mitochondrial DNA code</option>
33 <option value="8">Euplotid Nuclear code</option>
34 <option value="9">Alternative Yeast Nuclear code</option>
35 <option value="10">Ascidian mitochondrial DNA code</option>
36 <option value="11">Flatworm mitochondrial DNA code</option>
37 <option value="12">Blepharisma Nuclear code</option>
38 </param>
39 <conditional name="rate_cond">
40 <param name="rate" type="select" label="Rate variation">
41 <option value="1">None</option>
42 <option value="2">General Discrete</option>
43 <option value="3">Beta-Gamma</option>
44 </param>
45 <when value="1" />
46 <when value="2">
47 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
48 </when>
49 <when value="3">
50 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
51 </when>
52 </conditional>
53 <param name="branches" type="select" label="Set of branches to test">
54 <option value="1">All branches</option>
55 <option value="2">Internal branches</option>
56 <option value="3">Leaf branches</option>
57 <option value="4">Unlabeled branches</option>
58 </param>
59 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" /> 26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
60 </inputs> 27 </inputs>
61 <outputs> 28 <outputs>
62 <data name="meme_log" format="txt" /> 29 <data name="meme_log" format="txt" />
63 <data name="meme_output" format="json" from_work_dir="meme_input.fa.MEME.json" /> 30 <data name="meme_output" format="hyphy_json_results" from_work_dir="meme_input.fa.MEME.json" />
64 </outputs> 31 </outputs>
65 <tests> 32 <tests>
66 <test> 33 <test>
67 <param name="input_file" ftype="fasta" value="meme-in1.fa" /> 34 <param name="input_file" ftype="fasta" value="meme-in1.fa" />
68 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" /> 35 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" />