Mercurial > repos > stephenshank > hyphy_meme

annotate hyphy_meme.xml @ 1:e4c2b5776ea6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
author stephenshank
date Mon, 10 Sep 2018 15:14:49 -0400
parents 1a72da7a000d
children e44501a5cdcc
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1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
stephenshank
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1 <?xml version="1.0"?>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0">
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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3 <description>: Mixed Effects Model of Evolution</description>
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4 <macros>
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5 <import>macros.xml</import>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-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 $1}'</version_command>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 ln -s '$input_file' meme_input.fa &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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12 ln -s '$input_nhx' meme_input.nhx &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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13 echo $gencodeid > tool_params &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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14 echo `pwd`/meme_input.fa >> tool_params &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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15 echo `pwd`/meme_input.nhx >> tool_params &&
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16 echo '$branches' >> tool_params &&
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1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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17 echo '$p_value' >> tool_params &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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18 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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19 ]]>
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20 </command>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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21 <inputs>
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22 <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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23 <param name="input_nhx" type="data" format="nhx" label="Input newick file" />
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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24 <param name="gencodeid" type="select" label="Genetic code">
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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25 <option value="1">Universal code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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26 <option value="2">Vertebrate mitochondrial DNA code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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27 <option value="3">Yeast mitochondrial DNA code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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28 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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29 <option value="5">Invertebrate mitochondrial DNA code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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30 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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31 <option value="7">Echinoderm mitochondrial DNA code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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32 <option value="8">Euplotid Nuclear code</option>
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33 <option value="9">Alternative Yeast Nuclear code</option>
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34 <option value="10">Ascidian mitochondrial DNA code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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35 <option value="11">Flatworm mitochondrial DNA code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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36 <option value="12">Blepharisma Nuclear code</option>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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37 </param>
1
e4c2b5776ea6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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38 <param name="branches" type="select" label="Set of branches to test">
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39 <option value="1">All branches</option>
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40 <option value="2">Internal branches</option>
e4c2b5776ea6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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41 <option value="3">Leaf branches</option>
e4c2b5776ea6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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42 <option value="4">Unlabeled branches</option>
e4c2b5776ea6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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43 </param>
0
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44 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
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45 </inputs>
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46 <outputs>
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47 <data name="meme_log" format="txt" />
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48 <data name="meme_output" format="json" from_work_dir="meme_input.fa.MEME.json" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
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53 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
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54 <output name="meme_output" file="meme-out1.json" compare="sim_size" />
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55 </test>
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56 </tests>
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57 <help>
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58 <![CDATA[
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59 Detecting natural selection within protein coding genes is difficult to identify because selection is frequently transient or episodic. Existing computational techniques, which are designed to identify sites subject to pervasive selection, may fail to recognize sites where selection is episodic. MEME is capable of identifying instances of both episodic and pervasive positive selection at the level of an individual site.
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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60 ]]>
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61 </help>
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62 <expand macro="citations">
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63 <citation type="doi">10.1371/journal.pgen.1002764</citation>
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64 </expand>
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65 </tool>