Mercurial > repos > iuc > drep_dereplicate

annotate macros.xml @ 1:e9621d0f4e6b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:03:02 +0000
parents aba9d1e647b6
children 923c3bb71055
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aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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1 <macros>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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2 <token name="@VERSION@">2.5.4</token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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3 <xml name="requirements">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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4 <requirements>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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5 <requirement type="package" version="@VERSION@">drep</requirement>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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6 <yield/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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7 </requirements>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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8 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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9 <xml name="citations">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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10 <citations>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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11 <citation type="doi">10.1038/ismej.2017.126</citation>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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12 <yield />
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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13 </citations>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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14 </xml>
1
e9621d0f4e6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 <xml name="bio_tools">
e9621d0f4e6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 <xrefs>
e9621d0f4e6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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17 <xref type="bio.tools">drep</xref>
e9621d0f4e6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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18 </xrefs>
e9621d0f4e6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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19 </xml>
0
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20
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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21 <xml name="genomes">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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22 <param argument="--genomes" type="data" format="fasta" label="genomes fasta files" multiple="true"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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23 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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24 <token name="@PREPARE_GENOMES@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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25 #import re
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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26 #set $genomefiles = []
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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27 #for $genome in $genomes
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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28 #set $input_name = $re.sub('[^\w\-_.]', '_',str($genome.element_identifier.split('/')[-1]))
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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29 ln -s '${genome}' '${input_name}' &&
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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30 $genomefiles.append($input_name)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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31 #end for
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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32 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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33 <token name="@GENOMES@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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34 -g
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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35 #for $genomefile in $genomefiles
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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36 '${genomefile}'
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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37 #end for
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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38 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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39
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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40
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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41 <xml name="checkm_method">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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42 <param argument="--checkM_method" type="select" label="checkm method" optional="true">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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43 <option value="taxonomy_wf">taxonomy_wf (faster)</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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44 <option value="lineage_wf">lineage_wf (more accurate)</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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45 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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46 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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47 <token name="@CHECKM_METHOD@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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48 #if $checkM_method:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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49 --checkM_method $checkM_method
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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50 #end if
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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51 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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52
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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53 <xml name="filtering_options">
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54 <conditional name="filter">
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55 <param name="set_options" type="select" label="set filtering options">
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56 <option value="yes">Yes</option>
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57 <option value="no" selected="true">No (use --checkM_method taxonomy_wf)</option>
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58 </param>
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59 <when value="yes">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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60 <param argument="--length" type="integer" value="50000" label="Minimum genome length"/>
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61 <param argument="--completeness" type="integer" value="75" min="0" max="100" label="Minimum genome completeness percent"/>
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62 <param argument="--contamination" type="integer" value="25" min="0" max="100" label="Maximum genome contamination percent"/>
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63
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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64 <conditional name="quality">
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65 <param argument="source" type="select" label="genome quality">
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66 <help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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67 --ignoreGenomeQuality is useful with
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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68 bacteriophages or eukaryotes or things where checkM
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69 scoring does not work. Will only choose genomes based
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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70 on length and N50.
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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71 </help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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72 <option value="checkm" selected="true">Run checkM</option>
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73 <option value="genomeInfo">User supplied genomeInfo csv file</option>
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74 <option value="ignoreGenomeQuality">--ignoreGenomeQuality (NOT RECOMMENDED!)</option>
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75 </param>
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76 <when value="checkm">
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77 <param argument="--checkM_method" type="select" label="checkm method" optional="true">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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78 <help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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79 Using the checkm method of lineage_wf can require more than 40Gb of RAM.
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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80 </help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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81 <option value="taxonomy_wf">taxonomy_wf (faster)</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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82 <option value="lineage_wf">lineage_wf (more accurate)</option>
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83 </param>
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84 </when>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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85 <when value="genomeInfo">
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86 <param argument="--genomeInfo" type="data" format="csv" label="genomes fasta files">
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87 <help><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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88 A CSV dataset that must contain: [
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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89 "genome"(history dataset name of .fasta dataset of that genome),
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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parents:
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90 "completeness"(0-100 value for completeness of the genome),
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parents:
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91 "contamination"(0-100 value of the contamination of the genome)]
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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92 ]]></help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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93 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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94 </when>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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95 <when value="ignoreGenomeQuality"/>
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96 </conditional>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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97 </when>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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98 <when value="no"/>
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99 </conditional>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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100 </xml>
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101 <token name="@FILTER_OPTIONS@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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102 #if $filter.set_options == 'yes':
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103 --length $filter.length
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104 --completeness $filter.completeness
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105 --contamination $filter.contamination
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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106 #if $filter.quality.source == 'checkm'
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107 --checkM_method $filter.quality.checkM_method
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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108 #elif $filter.quality.source == 'genomeInfo'
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109 --genomeInfo $filter.quality.genomeInfo
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110 #elif $filter.quality.source == 'ignoreGenomeQuality'
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111 --ignoreGenomeQuality
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112 #end if
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113 #else
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114 --checkM_method taxonomy_wf
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115 #end if
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116 ]]></token>
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117
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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118 <xml name="genome_comparison_options">
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119 <conditional name="genome_comparison">
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120 <param name="set_options" type="select" label="set genome comparison options">
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121 <option value="yes">Yes</option>
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122 <option value="no" selected="true">No</option>
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123 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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124 <when value="yes">
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125 <param argument="--MASH_sketch" type="integer" value="1000" label="MASH sketch size"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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126 <param argument="--S_algorithm" type="select" label="Algorithm for secondary clustering comaprisons">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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127 <option value="ANImf" selected="true">ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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128 <option value="ANIn">ANIn = Align whole genomes with nucmer; compare aligned regions</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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129 <option value="gANI">gANI = Identify and align ORFs; compare aligned ORFS</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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130 </param>
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131 <param argument="-n_PRESET" type="select" label="Presets to pass to nucmer">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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132 <option value="normal" selected="true">normal = default ANIn parameters (default: normal)</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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133 <option value="tight">tight = only align highly conserved regions</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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134 </param>
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135 </when>
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136 <when value="no"/>
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137 </conditional>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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138 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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139 <token name="@GENOME_COMPARISON_OPTIONS@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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140 #if $genome_comparison.set_options == 'yes':
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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141 --MASH_sketch $genome_comparison.MASH_sketch
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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142 --S_algorithm $genome_comparison.S_algorithm
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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143 -n_PRESET $genome_comparison.n_PRESET
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144 #end if
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145 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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146
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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147 <xml name="clustering_options">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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148 <conditional name="clustering">
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149 <param name="set_options" type="select" label="set clustering options">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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150 <option value="yes">Yes</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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151 <option value="no" selected="true">No</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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152 </param>
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153 <when value="yes">
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154 <param argument="--P_ani" type="float" value="0.9" min="0." max="1." label="ANI threshold to form primary (MASH) clusters"/>
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155 <param argument="--S_ani" type="float" value="0.99" min="0." max="1." label="ANI threshold to form secondary clusters"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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156
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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157 <param argument="--SkipMash" type="boolean" truevalue="--SkipMash" falsevalue="" checked="false" label="Skip MASH clustering, just do secondary clustering on all genomes"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
158 <param argument="--SkipSecondary" type="boolean" truevalue="--SkipSecondary" falsevalue="" checked="false" label="Skip secondary clustering, just perform MASH clustering"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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159 <param argument="--cov_thresh" type="float" value="0.1" min="0." max="1." label="Minmum level of overlap between genomes when doing secondary comparisons"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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160 <param argument="--coverage_method" type="select" label="Method to calculate coverage of an alignment">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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161 <help>(for ANIn/ANImf only; gANI can only do larger method)</help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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162 <option value="larger" selected="true">arger = max((aligned length / genome 1), (aligned_length / genome2))</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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163 <option value="total">total = 2*(aligned length) / (sum of total genome lengths)</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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164 </param>
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165 <param argument="--clusterAlg" type="select" label="Algorithm used to cluster genomes">
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166 <help>(passed to scipy.cluster.hierarchy.linkage)</help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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167 <option value="average" selected="true">average</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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168 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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169 </when>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
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170 <when value="no"/>
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171 </conditional>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
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172 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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173 <token name="@CLUSTERING_OPTIONS@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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174 #if $clustering.set_options == 'yes':
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iuc
parents:
diff changeset
175 --P_ani $clustering.P_ani
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
176 --S_ani $clustering.S_ani
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
177 $clustering.SkipMash
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
178 $clustering.SkipSecondary
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
179 --cov_thresh $clustering.cov_thresh
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
180 --coverage_method $clustering.coverage_method
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
181 --clusterAlg $clustering.clusterAlg
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
182 #end if
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
183 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
184
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
185 <xml name="scoring_options">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
186 <conditional name="scoring">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
187 <param name="set_options" type="select" label="set scoring options">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
188 <option value="yes">Yes</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
189 <option value="no" selected="true">No</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
190 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
191 <when value="yes">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
192 <param argument="--completeness_weight" type="float" value="1" label="completeness weight">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
193 <help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
194 Based off of the formula:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
195 A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
196 A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight;
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
197 </help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
198 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
199 <param argument="--contamination_weight" type="float" value="5" label="contamination weight"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
200 <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="strain heterogeneity weight"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
201 <param argument="--N50_weight" type="float" value=".5" label="weight of log(genome N50)"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
202 <param argument="--size_weight" type="float" value="0" label="weight of log(genome size)"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
203 </when>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
204 <when value="no"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
205 </conditional>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
206 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
207 <token name="@SCORING_OPTIONS@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
208 #if $scoring.set_options == 'yes':
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
209 --completeness_weight $scoring.completeness_weight
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
210 --contamination_weight $scoring.contamination_weight
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
211 --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
212 --N50_weight $scoring.N50_weight
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
213 --size_weight $scoring.size_weight
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
214 #end if
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
215 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
216
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
217 <xml name="taxonomy_options">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
218 <conditional name="taxonomy">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
219 <param name="set_options" type="select" label="generate taxonomy information">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
220 <option value="yes">Yes</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
221 <option value="no" selected="true">No</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
222 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
223 <when value="yes">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
224 <param argument="--tax_method" type="select" label="Method of determining taxonomy">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
225 <help>(for ANIn/ANImf only; gANI can only do larger method)</help>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
226 <option value="percent" selected="true">percent = The most descriptive taxonimic level with at least (per) hits</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
227 <option value="max">max = The centrifuge taxonomic level with the most overall hits</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
228 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
229 <param argument="--percent" type="float" value="50" min="0" max="100" label="minimum percent for percent method"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
230 <param argument="--cent_index" type="data" format="" label="centrifuge index"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
231 </when>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
232 <when value="no"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
233 </conditional>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
234 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
235 <token name="@TAXONOMY_OPTIONS@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
236 #if $taxonomy.set_options == 'yes':
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
237 --run_tax
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
238 --tax_method $taxonomy.tax_method
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
239 --percent $taxonomy.percent
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
240 --cent_index $taxonomy.cent_index
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
241 #end if
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
242 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
243
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
244 <xml name="warning_options">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
245 <conditional name="warning">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
246 <param name="set_options" type="select" label="set warning options">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
247 <option value="yes">Yes</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
248 <option value="no" selected="true">No</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
249 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
250 <when value="yes">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
251 <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="How far from the threshold to throw cluster warnings"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
252 <param argument="--warn_sim" type="float" value="0.98" min="0" max="1" label="Similarity threshold for warnings between dereplicated genomes"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
253 <param argument="--warn_aln" type="float" value="0.25" min="0" max="1" label="Minimum aligned fraction for warnings between dereplicated genomes (ANIn)"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
254 </when>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
255 <when value="no"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
256 </conditional>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
257 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
258 <token name="@WARNING_OPTIONS@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
259 #if $warning.set_options == 'yes':
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
260 --warn_dist $warning.warn_dist
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
261 --warn_sim $warning.warn_sim
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
262 --warn_aln $warning.warn_aln
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
263 #end if
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
264 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
265
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
266 <xml name="select_outputs">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
267 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
268 <option value="log" selected="true">log</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
269 <option value="warnings" selected="true">Warnings</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
270 <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
271 <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
272 <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
273 <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
274 <yield/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
275 </param>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
276 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
277 <xml name="select_drep_outputs">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
278 <expand macro="select_outputs">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
279 <option value="Cluster_scoring">Cluster_scoring.pdf</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
280 <option value="Winning_genomes">Winning_genomes.pdf</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
281 <option value="Widb">Widb.csv</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
282 <option value="Chdb">Chdb.tsv</option>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
283 </expand>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
284 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
285
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
286 <xml name="common_outputs">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
287 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
288 <filter>'log' in select_outputs or not select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
289 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
290 <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Warnings" from_work_dir="outdir/log/warnings.txt">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
291 <filter>'warnings' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
292 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
293 <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
294 <filter>'Primary_clustering_dendrogram' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
295 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
296 <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
297 <filter>'Secondary_clustering_dendrograms' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
298 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
299 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
300 <filter>'Secondary_clustering_MDS' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
301 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
302 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
303 <filter>'Clustering_scatterplots' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
304 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
305 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
306
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
307
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
308 <xml name="drep_outputs">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
309 <expand macro="common_outputs"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
310 <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
311 <filter>'Cluster_scoring' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
312 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
313 <data name="Winning_genomes" format="pdf" label="${tool.name} on ${on_string}: Winning_genomes.pdf" from_work_dir="outdir/figures/Winning_genomes.pdf">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
314 <filter>'Winning_genomes' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
315 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
316 <data name="Widb" format="csv" label="${tool.name} on ${on_string}: Widb.csv" from_work_dir="outdir/data_tables/Widb.csv">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
317 <filter>'Widb' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
318 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
319 <data name="Chdb" format="tabular" label="${tool.name} on ${on_string}: Chdb.tsv" from_work_dir="outdir/data/checkM/checkM_outdir/Chdb.tsv">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
320 <filter>'Chdb' in select_outputs</filter>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
321 </data>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
322 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
323
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
324
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
325 <xml name="test_defaults_log">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
326 <test>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
327 <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
328 <output name="log">
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
329 <assert_contents>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
330 <yield/>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
331 </assert_contents>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
332 </output>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
333 </test>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
334 </xml>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
335
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
336 <token name="@GENOMES_HELP@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
337 I/O PARAMETERS:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
338 -g [GENOMES [GENOMES ...]], --genomes [GENOMES [GENOMES ...]]
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
339 genomes to cluster in .fasta format
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
340 (default: None)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
341
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
342
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
343 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
344
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
345 <token name="@FILTERING_HELP@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
346 FILTERING OPTIONS:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
347 -l LENGTH, --length LENGTH
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
348 Minimum genome length
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
349 (default: 50000)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
350
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
351
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
352 -comp COMPLETENESS, --completeness COMPLETENESS
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
353 Minumum genome completeness
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
354 (default: 75)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
355
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
356
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
357 -con CONTAMINATION, --contamination CONTAMINATION
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
358 Maximum genome contamination
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
359 (default: 25)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
360
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
361
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
362 --ignoreGenomeQuality
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
363 Don't run checkM or do any quality filtering. NOT
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
364 RECOMMENDED! This is useful for use with
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
365 bacteriophages or eukaryotes or things where checkM
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
366 scoring does not work. Will only choose genomes based
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
367 on length and N50 (default: False)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
368
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
369
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
370 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
371
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
372 <token name="@GENOME_COMPARISON_HELP@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
373 GENOME COMPARISON PARAMETERS:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
374 -ms MASH_SKETCH, --MASH_sketch MASH_SKETCH
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
375 MASH sketch size (default: 1000)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
376
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
377 --S_algorithm {goANI,ANIn,ANImf,gANI}
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
378 Algorithm for secondary clustering comaprisons:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
379 ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
380 ANIn = Align whole genomes with nucmer; compare aligned regions
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
381 gANI = Identify and align ORFs; compare aligned ORFS
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
382 (default: ANImf)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
383
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
384 -n_PRESET {normal,tight}
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
385 Presets to pass to nucmer
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
386 tight = only align highly conserved regions
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
387 normal = default ANIn parameters (default: normal)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
388
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
389 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
390
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
391 <token name="@CLUSTERING_HELP@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
392 CLUSTERING PARAMETERS:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
393 -pa P_ANI, --P_ani P_ANI
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
394 ANI threshold to form primary (MASH) clusters
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
395 (default: 0.9)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
396 -sa S_ANI, --S_ani S_ANI
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
397 ANI threshold to form secondary clusters
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
398 (default: 0.99)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
399
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
400 --SkipMash Skip MASH clustering, just do secondary clustering on
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
401 all genomes (default: False)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
402 --SkipSecondary Skip secondary clustering, just perform MASH clustering
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
403 (default: False)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
404
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
405 -nc COV_THRESH, --cov_thresh COV_THRESH
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
406 Minmum level of overlap between genomes when doing
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
407 secondary comparisons (default: 0.1)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
408 -cm {total,larger}, --coverage_method {total,larger}
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
409 Method to calculate coverage of an alignment
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
410 (for ANIn/ANImf only; gANI can only do larger method)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
411 total = 2*(aligned length) / (sum of total genome lengths)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
412 larger = max((aligned length / genome 1), (aligned_length / genome2))
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
413 (default: larger)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
414
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
415 --clusterAlg CLUSTERALG
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
416 Algorithm used to cluster genomes (passed to
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
417 scipy.cluster.hierarchy.linkage (default: average)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
418
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
419 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
420
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
421 <token name="@SCORING_HELP@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
422 SCORING CRITERIA
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
423 Based off of the formula:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
424 A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
425
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
426 A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
427 -comW COMPLETENESS_WEIGHT, --completeness_weight COMPLETENESS_WEIGHT
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
428 completeness weight (default: 1)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
429 -conW CONTAMINATION_WEIGHT, --contamination_weight CONTAMINATION_WEIGHT
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
430 contamination weight (default: 5)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
431 -strW STRAIN_HETEROGENEITY_WEIGHT, --strain_heterogeneity_weight STRAIN_HETEROGENEITY_WEIGHT
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
432 strain heterogeneity weight (default: 1)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
433 -N50W N50_WEIGHT, --N50_weight N50_WEIGHT
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
434 weight of log(genome N50) (default: 0.5)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
435 -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
436 weight of log(genome size) (default: 0)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
437
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
438
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
439 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
440
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
441 <token name="@TAXONOMY_HELP@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
442 TAXONOMY:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
443 --run_tax generate taxonomy information (Tdb)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
444 (default: False)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
445
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
446 --tax_method {percent,max}
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
447 Method of determining taxonomy
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
448 percent = The most descriptive taxonimic level with at least (per) hits
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
449 max = The centrifuge taxonomic level with the most overall hits
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
450 (default: percent)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
451
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
452
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
453 -per PERCENT, --percent PERCENT
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
454 minimum percent for percent method
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
455 (default: 50)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
456
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
457
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
458 --cent_index CENT_INDEX
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
459 path to centrifuge index (for example,
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
460 /home/mattolm/download/centrifuge/indices/b+h+v
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
461 (default: None)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
462
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
463 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
464
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
465 <token name="@WARNINGS_HELP@"><![CDATA[
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
466 WARNINGS:
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
467 --warn_dist WARN_DIST
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
468 How far from the threshold to throw cluster warnings
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
469 (default: 0.25)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
470 --warn_sim WARN_SIM Similarity threshold for warnings between dereplicated
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
471 genomes (default: 0.98)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
472 --warn_aln WARN_ALN Minimum aligned fraction for warnings between
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
473 dereplicated genomes (ANIn) (default: 0.25)
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
474
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
475 ]]></token>
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
476
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
477
aba9d1e647b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
478 </macros>