Mercurial > repos > rdvelazquez > hyphy_busted
diff macros.xml @ 4:f8abbbc7e29e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
| author | rdvelazquez |
|---|---|
| date | Fri, 07 Jun 2019 10:18:17 -0400 |
| parents | d0a3511a8f33 |
| children |
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--- a/macros.xml Mon Feb 18 15:14:26 2019 -0500 +++ b/macros.xml Fri Jun 07 10:18:17 2019 -0400 @@ -6,50 +6,43 @@ </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> + <option value="Universal">Universal code</option> + <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA code</option> + <option value="Yeast-mtDNA">Yeast mitochondrial DNA code</option> + <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> + <option value="Invertebrate-mtDNA">Invertebrate mitochondrial DNA code</option> + <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and Hexamita Nuclear code</option> + <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA code</option> + <option value="Euplotid-Nuclear">Euplotid Nuclear code</option> + <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear code</option> + <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA code</option> + <option value="Flatworm-mtDNA,">Flatworm mitochondrial DNA code</option> + <option value="Blepharisma-Nuclear">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> + <option value="All">All branches</option> + <option value="Internal">Internal branches</option> + <option value="Leaves">Leaf branches</option> + <option value="'Unlabeled-branches'">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> <yield/> </citations> </xml> - <token name="@VERSION@">2.3.14</token> + <token name="@VERSION@">2.5.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement> <yield/> </requirements> </xml> - <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` && + <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` && export HYPHY_PATH=`dirname \$HYPHY` && 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:-2} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token> + <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | hyphy LIBPATH=\$HYPHY_LIB ]]></token> </macros>