Mercurial > repos > rdvelazquez > hyphy_gard
diff macros.xml @ 2:9e533457ebc0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
| author | rdvelazquez |
|---|---|
| date | Mon, 18 Feb 2019 15:12:22 -0500 |
| parents | e489b7f00db7 |
| children | 9640a5b51502 |
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--- a/macros.xml Tue Dec 04 11:12:01 2018 -0500 +++ b/macros.xml Mon Feb 18 15:12:22 2019 -0500 @@ -1,5 +1,36 @@ <?xml version="1.0"?> <macros> + <xml name="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"/> + </xml> + <xml name="gencode"> + <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> + </xml> + <xml name="branches"> + <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> + </xml> + <xml name="version_command"> + <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/bti079</citation> @@ -9,17 +40,16 @@ <token name="@VERSION@">2.3.14</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@"> - hyphy</requirement> + <requirement type="package" version="@VERSION@">hyphy</requirement> <yield/> </requirements> </xml> - <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` && + <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` && export HYPHY_PATH=`dirname \$HYPHY` && -export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` && -cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token> +export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token> + <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token> <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` && export HYPHYMPI_PATH=`dirname \$HYPHYMPI` && export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` && -cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token> +cat tool_params | mpirun -np \${GALAXY_SLOTS:-2} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token> </macros>