Mercurial > repos > rdvelazquez > hyphy_meme
diff hyphy_meme.xml @ 1:cffd8bd6e3ec draft
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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--- a/hyphy_meme.xml Tue Dec 04 10:45:43 2018 -0500 +++ b/hyphy_meme.xml Mon Feb 11 14:31:06 2019 -0500 @@ -5,7 +5,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + <expand macro="version_command" /> <command detect_errors="exit_code"> <![CDATA[ export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} && @@ -20,47 +20,14 @@ ]]> </command> <inputs> - <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> - <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> - <param name="gencodeid" type="select" label="Genetic code"> - <option value="1">Universal code</option> - <option value="2">Vertebrate mitochondrial DNA code</option> - <option value="3">Yeast mitochondrial DNA code</option> - <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> - <option value="5">Invertebrate mitochondrial DNA code</option> - <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> - <option value="7">Echinoderm mitochondrial DNA code</option> - <option value="8">Euplotid Nuclear code</option> - <option value="9">Alternative Yeast Nuclear code</option> - <option value="10">Ascidian mitochondrial DNA code</option> - <option value="11">Flatworm mitochondrial DNA code</option> - <option value="12">Blepharisma Nuclear code</option> - </param> - <conditional name="rate_cond"> - <param name="rate" type="select" label="Rate variation"> - <option value="1">None</option> - <option value="2">General Discrete</option> - <option value="3">Beta-Gamma</option> - </param> - <when value="1" /> - <when value="2"> - <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" /> - </when> - <when value="3"> - <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" /> - </when> - </conditional> - <param name="branches" type="select" label="Set of branches to test"> - <option value="1">All branches</option> - <option value="2">Internal branches</option> - <option value="3">Leaf branches</option> - <option value="4">Unlabeled branches</option> - </param> + <expand macro="inputs" /> + <expand macro="gencode" /> + <expand macro="branches" /> <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" /> </inputs> <outputs> <data name="meme_log" format="txt" /> - <data name="meme_output" format="json" from_work_dir="meme_input.fa.MEME.json" /> + <data name="meme_output" format="hyphy_json_results" from_work_dir="meme_input.fa.MEME.json" /> </outputs> <tests> <test>