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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit d4006c1381bdece9d754bdfebb80efb61040d6e9-dirty
author veg
date Wed, 18 Apr 2018 16:28:28 -0400
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a3f7993dca52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit d4006c1381bdece9d754bdfebb80efb61040d6e9-dirty
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1 <?xml version="1.0"?>
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2 <tool id="mmvc" version="1.0.2" name="mmvc">
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3 <description>Multinomial mixture variant caller</description>
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4 <requirements>
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5 <requirement type="package" version="1.0.2">mmvc</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:"/>
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9 </stdio>
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10 <version_command/>
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11 <command><![CDATA[
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12 mmvc -j '$json_report' -f '$filter_msa'
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13 #if str($options.advanced) == 'advanced':
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14 -g $options.grid_density -c $options.chain_length -b $options.burnin_fraction -t $options.target_rate -p $options.posterior_threshold
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15 #end if
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16 '$input_fasta'
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17 ]]></command>
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18 <inputs>
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19 <param name="input_fasta" label="Input FASTA" type="data" format="fasta"/>
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20 <conditional name="options">
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21 <param label="Additional options" name="advanced" type="select">
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22 <option value="defaults">Use defaults</option>
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23 <option value="advanced">Specify additional parameters</option>
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24 </param>
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25 <when value="defaults"/>
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26 <when value="advanced">
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27 <param label="GRID_DENSITY" name="grid_density" type="integer" value="10"/>
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28 <param label="CHAIN_LENGTH" name="chain_length" type="integer" value="2000000"/>
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29 <param label="BURNIN_FRACTION" name="burnin_fraction" type="float" value="0.5"/>
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30 <param label="TARGET_RATE" name="target_rate" type="float" value="0.01"/>
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31 <param label="POSTERIOR_THRESHOLD" name="posterior_threshold" type="float" value="0.95"/>
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32 </when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 <data format="json" name="json_report"/>
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37 <data format="fasta" name="filter_msa"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input_fasta" value="mmvc-in1.fa"/>
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42 <param name="advanced" value="advanced"/>
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43 <param name="chain_length" value="200"/>
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44 <output name="json_report">
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45 <assert_contents>
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46 <has_text text="variant"/>
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47 <has_text text="weight"/>
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48 </assert_contents>
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49 </output>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53
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54 MMVC
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55 ----
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56 Multinomial mixture variant caller
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57
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58 ]]></help>
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59 <citations>
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60 <citation type="bibtex">
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61 @UNPUBLISHED{spond,
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62 author = "Sergei Kosakovsky Pond",
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63 title = "HyPhy: Hypothesis Testing using Phylogenies",
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64 year = "2000",
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65 note = "http://hyphy.org/",
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66 url = "http://hyphy.org/"}
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67 </citation>
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68 </citations>
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69 </tool>