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annotate macros.xml @ 8:070a1988e661 draft

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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 15:11:29 -0500
parents a7305e34418f
children 4377e155b9d1
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bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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1 <?xml version="1.0"?>
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2 <macros>
8
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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="1">Universal code</option>
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10 <option value="2">Vertebrate mitochondrial DNA code</option>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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11 <option value="3">Yeast mitochondrial DNA code</option>
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12 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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13 <option value="5">Invertebrate mitochondrial DNA code</option>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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14 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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15 <option value="7">Echinoderm mitochondrial DNA code</option>
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16 <option value="8">Euplotid Nuclear code</option>
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17 <option value="9">Alternative Yeast Nuclear code</option>
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18 <option value="10">Ascidian mitochondrial DNA code</option>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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19 <option value="11">Flatworm mitochondrial DNA code</option>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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20 <option value="12">Blepharisma Nuclear code</option>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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21 </param>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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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="1">All branches</option>
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26 <option value="2">Internal branches</option>
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27 <option value="3">Leaf branches</option>
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28 <option value="4">Unlabeled branches</option>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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29 </param>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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30 </xml>
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31 <xml name="version_command">
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32 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
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33 </xml>
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34 <xml name="citations">
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35 <citations>
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36 <citation type="doi">10.1093/bioinformatics/bti079</citation>
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37 <yield/>
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38 </citations>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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39 </xml>
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40 <token name="@VERSION@">2.3.14</token>
070a1988e661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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41 <xml name="requirements">
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42 <requirements>
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43 <requirement type="package" version="@VERSION@">hyphy</requirement>
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44 <yield/>
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45 </requirements>
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46 </xml>
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47 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` &&
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48 export HYPHY_PATH=`dirname \$HYPHY` &&
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49 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
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50 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
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51 <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` &&
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52 export HYPHYMPI_PATH=`dirname \$HYPHYMPI` &&
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53 export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` &&
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54 cat tool_params | mpirun -np \${GALAXY_SLOTS:-2} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token>
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55 </macros>