Mercurial > repos > stephenshank > hyphy_meme

annotate hyphy_meme.xml @ 2:e44501a5cdcc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
author stephenshank
date Tue, 30 Oct 2018 10:57:16 -0400
parents e4c2b5776ea6
children 3b7f2dbb5c44
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0">
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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>
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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 $1}'</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
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12 ln -s '$input_file' meme_input.fa &&
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13 ln -s '$input_nhx' meme_input.nhx &&
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14 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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15 echo `pwd`/meme_input.fa >> tool_params &&
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16 echo `pwd`/meme_input.nhx >> tool_params &&
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17 echo $branches >> tool_params &&
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18 echo $p_value >> tool_params &&
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19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
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24 <param name="input_nhx" type="data" format="nhx" label="Input newick file" />
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25 <param name="gencodeid" type="select" label="Genetic code">
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26 <option value="1">Universal code</option>
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27 <option value="2">Vertebrate mitochondrial DNA code</option>
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28 <option value="3">Yeast mitochondrial DNA code</option>
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29 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
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30 <option value="5">Invertebrate mitochondrial DNA code</option>
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31 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
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32 <option value="7">Echinoderm mitochondrial DNA code</option>
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33 <option value="8">Euplotid Nuclear code</option>
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34 <option value="9">Alternative Yeast Nuclear code</option>
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35 <option value="10">Ascidian mitochondrial DNA code</option>
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36 <option value="11">Flatworm mitochondrial DNA code</option>
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37 <option value="12">Blepharisma Nuclear code</option>
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38 </param>
2
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39 <conditional name="rate_cond">
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40 <param name="rate" type="select" label="Rate variation">
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41 <option value="1">None</option>
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42 <option value="2">General Discrete</option>
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43 <option value="3">Beta-Gamma</option>
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44 </param>
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45 <when value="1" />
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46 <when value="2">
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47 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
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48 </when>
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49 <when value="3">
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50 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
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51 </when>
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52 </conditional>
1
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53 <param name="branches" type="select" label="Set of branches to test">
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54 <option value="1">All branches</option>
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55 <option value="2">Internal branches</option>
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56 <option value="3">Leaf branches</option>
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57 <option value="4">Unlabeled branches</option>
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58 </param>
0
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59 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
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60 </inputs>
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61 <outputs>
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62 <data name="meme_log" format="txt" />
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63 <data name="meme_output" format="json" from_work_dir="meme_input.fa.MEME.json" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="input_file" ftype="fasta" value="meme-in1.fa" />
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68 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" />
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69 <param name="branches" value="1" />
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70 <param name="p_value" value="0.1" />
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71 <output name="meme_output" file="meme-out1.json" compare="sim_size" />
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72 </test>
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73 </tests>
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74 <help>
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75 <![CDATA[
2
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76 MEME employs a mixed-effects maximum likelihood approach to test the hypothesis that individual sites have been subject to episodic positive or diversifying selection. In other words, MEME aims to detect sites evolving under positive selection under a proportion of branches.
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77 ]]>
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78 </help>
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79 <expand macro="citations">
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80 <citation type="doi">10.1371/journal.pgen.1002764</citation>
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81 </expand>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
stephenshank
parents:
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82 </tool>