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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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acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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1 <?xml version="1.0"?>
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2 <macros>
3
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3 <xml name="inputs">
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4 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
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5 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
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6 </xml>
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7 <xml name="gencode">
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8 <param name="gencodeid" type="select" label="Genetic code">
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9 <option value="Universal">Universal code</option>
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10 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA code</option>
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11 <option value="Yeast-mtDNA">Yeast mitochondrial DNA code</option>
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12 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
f8abbbc7e29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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13 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial DNA code</option>
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14 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
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15 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA code</option>
f8abbbc7e29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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16 <option value="Euplotid-Nuclear">Euplotid Nuclear code</option>
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17 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear code</option>
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18 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA code</option>
f8abbbc7e29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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19 <option value="Flatworm-mtDNA,">Flatworm mitochondrial DNA code</option>
f8abbbc7e29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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20 <option value="Blepharisma-Nuclear">Blepharisma Nuclear code</option>
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21 </param>
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22 </xml>
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23 <xml name="branches">
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24 <param name="branches" type="select" label="Set of branches to test">
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25 <option value="All">All branches</option>
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26 <option value="Internal">Internal branches</option>
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27 <option value="Leaves">Leaf branches</option>
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28 <option value="'Unlabeled-branches'">Unlabeled branches</option>
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29 </param>
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30 </xml>
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31 <xml name="citations">
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32 <citations>
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33 <citation type="doi">10.1093/bioinformatics/bti079</citation>
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34 <yield/>
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35 </citations>
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36 </xml>
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37 <token name="@VERSION@">2.5.0</token>
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38 <xml name="requirements">
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39 <requirements>
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40 <requirement type="package" version="@VERSION@">hyphy</requirement>
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41 <yield/>
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42 </requirements>
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43 </xml>
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44 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
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45 export HYPHY_PATH=`dirname \$HYPHY` &&
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46 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
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47 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | hyphy LIBPATH=\$HYPHY_LIB ]]></token>
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48 </macros>