Mercurial > repos > rdvelazquez > hyphy_busted

annotate hyphy_busted.xml @ 1:8686dd081ecf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
author rdvelazquez
date Tue, 08 Jan 2019 10:56:06 -0500
parents acaa45acbf91
children 0d4341fca959
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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"?>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0">
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3 <description>: Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
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4 <macros>
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5 <import>macros.xml</import>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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6 </macros>
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7 <expand macro="requirements" />
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8 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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11 ln -s '$input_file' busted_input.fa &&
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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12 ln -s '$input_nhx' busted_input.nhx &&
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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13 echo $gencodeid > tool_params &&
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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14 echo `pwd`/busted_input.fa >> tool_params &&
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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15 echo `pwd`/busted_input.nhx >> tool_params &&
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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16 echo '$branches' >> tool_params &&
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf > '$busted_log'
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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22 <param name="input_nhx" type="data" format="nhx" label="Input newick file" />
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23 <param name="gencodeid" type="select" label="Genetic code">
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24 <option value="1">Universal code</option>
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25 <option value="2">Vertebrate mitochondrial DNA code</option>
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26 <option value="3">Yeast mitochondrial DNA code</option>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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27 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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28 <option value="5">Invertebrate mitochondrial DNA code</option>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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29 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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30 <option value="7">Echinoderm mitochondrial DNA code</option>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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31 <option value="8">Euplotid Nuclear code</option>
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32 <option value="9">Alternative Yeast Nuclear code</option>
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33 <option value="10">Ascidian mitochondrial DNA code</option>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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34 <option value="11">Flatworm mitochondrial DNA code</option>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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35 <option value="12">Blepharisma Nuclear code</option>
acaa45acbf91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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36 </param>
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37 <param name="branches" type="select" label="Set of branches to test">
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38 <option value="1">All branches</option>
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39 <option value="2">Internal branches</option>
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40 <option value="3">Leaf branches</option>
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41 <option value="4">Unlabeled branches</option>
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42 </param>
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43 </inputs>
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44 <outputs>
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45 <data name="busted_log" format="txt" />
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46 <data name="busted_output" format="json" from_work_dir="busted_input.fa.BUSTED.json" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
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51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
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52 <output name="busted_output" file="busted-out1.json" compare="sim_size" />
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53 </test>
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54 </tests>
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55 <help>
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56 <![CDATA[
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57 BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection.
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58 ]]>
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59 </help>
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60 <expand macro="citations">
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61 <citation type="doi">10.1093/molbev/msv035</citation>
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62 </expand>
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63 </tool>