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annotate mmvc.xml @ 2:12e4a2e84931 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'-dirty
author rdvelazquez
date Fri, 15 Mar 2019 13:43:59 -0400
parents c5c1faa433e4
children
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c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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1 <?xml version="1.0"?>
2
12e4a2e84931 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'-dirty
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2 <tool id="mmvc" version="1.0.2" name="mmvc">
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c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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3 <description>Multinomial mixture variant caller</description>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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4 <requirements>
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5 <requirement type="package" version="1.0.2">mmvc</requirement>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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6 </requirements>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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7 <stdio>
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8 <exit_code range="1:"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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9 </stdio>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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10 <version_command/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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11 <command><![CDATA[
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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12 mmvc -j '$json_report' -f '$filter_msa'
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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13 #if str($options.advanced) == 'advanced':
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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14 -g $options.grid_density -c $options.chain_length -b $options.burnin_fraction -t $options.target_rate -p $options.posterior_threshold
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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15 #end if
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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16 '$input_fasta' &&
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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17 $__tool_directory__/extract_mmvc_consensus '$json_report' '$input_fasta.display_name' '$consensus_fasta'
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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18 ]]></command>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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19 <inputs>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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20 <param name="input_fasta" label="Input FASTA" type="data" format="fasta"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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21 <conditional name="options">
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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22 <param label="Additional options" name="advanced" type="select">
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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23 <option value="defaults">Use defaults</option>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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24 <option value="advanced">Specify additional
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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25 parameters</option>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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26 </param>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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27 <when value="defaults"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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28 <when value="advanced">
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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29 <param label="GRID_DENSITY" name="grid_density" type="integer" value="10"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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30 <param label="CHAIN_LENGTH" name="chain_length" type="integer" value="2000000"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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31 <param label="BURNIN_FRACTION" name="burnin_fraction" type="float" value="0.5"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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32 <param label="TARGET_RATE" name="target_rate" type="float" value="0.01"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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33 <param label="POSTERIOR_THRESHOLD" name="posterior_threshold" type="float" value="0.95"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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34 </when>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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35 </conditional>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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36 </inputs>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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37 <outputs>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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38 <data format="json" name="json_report"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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39 <data format="fasta" name="filter_msa"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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40 <data format="fasta" name="consensus_fasta"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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41 </outputs>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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42 <tests>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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43 <test>
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44 <param name="input_fasta" value="mmvc-in1.fa"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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45 <param name="advanced" value="advanced"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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46 <param name="chain_length" value="200"/>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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47 <output name="json_report">
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48 <assert_contents>
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49 <has_text text="variant"/>
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50 <has_text text="weight"/>
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51 </assert_contents>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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52 </output>
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53 </test>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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54 </tests>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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55 <help><![CDATA[
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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56 MMVC
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57 ----
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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58 Multinomial mixture variant caller
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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59 ]]></help>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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60 <citations>
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61 <citation type="bibtex">@UNPUBLISHED{spond, author = "Sergei
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62 Kosakovsky Pond", title = "HyPhy: Hypothesis Testing using
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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63 Phylogenies", year = "2000", note = "http://hyphy.org/", url =
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64 "http://hyphy.org/"}</citation>
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
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65 </citations>
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66 </tool>