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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep"
author jjohnson
date Fri, 24 Jan 2020 10:24:51 -0500
parents cb2fc9f60381
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
1 <macros>
3
3f7c9be3edde "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep"
jjohnson
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2 <token name="@VERSION@">2.4.0</token>
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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3 <xml name="requirements">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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4 <requirements>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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5 <requirement type="package" version="@VERSION@">drep</requirement>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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6 <yield/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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7 </requirements>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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8 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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9 <xml name="citations">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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10 <citations>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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11 <citation type="doi">10.1038/ismej.2017.126</citation>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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12 <yield />
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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13 </citations>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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14 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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15
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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16
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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17 <xml name="genomes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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18 <param argument="--genomes" type="data" format="fasta" label="genomes fasta files" multiple="true"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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19 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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20 <token name="@PREPARE_GENOMES@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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21 #import re
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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22 #set $genomefiles = []
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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23 #for $genome in $genomes
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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24 #set $input_name = $re.sub('[^\w\-_.]', '_',str($genome.element_identifier.split('/')[-1]))
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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25 ln -s '${genome}' '${input_name}' &&
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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26 $genomefiles.append($input_name)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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27 #end for
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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28 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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29 <token name="@GENOMES@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
30 -g
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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31 #for $genomefile in $genomefiles
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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32 '${genomefile}'
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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33 #end for
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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34 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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35
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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36
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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37 <xml name="checkm_method">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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38 <param argument="--checkM_method" type="select" label="checkm method" optional="true">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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39 <option value="lineage_wf">lineage_wf (more accurate)</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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40 <option value="taxonomy_wf">taxonomy_wf (faster)</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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41 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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42 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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43 <token name="@CHECKM_METHOD@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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44 #if $checkM_method:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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45 --checkM_method $checkM_method
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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46 #end if
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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47 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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48
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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49 <xml name="filtering_options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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50 <conditional name="filter">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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51 <param name="set_options" type="select" label="set filtering options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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52 <option value="yes">Yes</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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53 <option value="no" selected="true">No</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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54 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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55 <when value="yes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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56 <param argument="--length" type="integer" value="50000" label="Minimum genome length"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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57 <param argument="--completeness" type="integer" value="75" min="0" max="100" label="Minimum genome completeness percent"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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58 <param argument="--contamination" type="integer" value="25" min="0" max="100" label="Maximum genome contamination percent"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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59
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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60 <conditional name="quality">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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61 <param argument="source" type="select" label="genome quality">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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62 <help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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63 --ignoreGenomeQuality is useful with
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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64 bacteriophages or eukaryotes or things where checkM
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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65 scoring does not work. Will only choose genomes based
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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66 on length and N50.
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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67 </help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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68 <option value="checkm" selected="true">Run checkM</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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69 <option value="genomeInfo">User supplied genomeInfo csv file</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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70 <option value="ignoreGenomeQuality">--ignoreGenomeQuality (NOT RECOMMENDED!)</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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71 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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72 <when value="checkm">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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73 <param argument="--checkM_method" type="select" label="checkm method" optional="true">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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74 <option value="lineage_wf">lineage_wf (more accurate)</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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75 <option value="taxonomy_wf">taxonomy_wf (faster)</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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76 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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77 </when>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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78 <when value="genomeInfo">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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79 <param argument="--genomeInfo" type="data" format="csv" label="genomes fasta files">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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80 <help><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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81 A CSV dataset that must contain: [
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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82 "genome"(history dataset name of .fasta dataset of that genome),
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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83 "completeness"(0-100 value for completeness of the genome),
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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84 "contamination"(0-100 value of the contamination of the genome)]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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85 ]]></help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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86 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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87 </when>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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88 <when value="ignoreGenomeQuality"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
89 </conditional>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
90
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
91 </when>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
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92 <when value="no"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
93 </conditional>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
94 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
95 <token name="@FILTER_OPTIONS@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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96 #if $filter.set_options == 'yes':
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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97 --length $filter.length
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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98 --completeness $filter.completeness
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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99 --contamination $filter.contamination
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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100 #if $filter.quality.source == 'checkm'
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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101 --checkM_method $filter.quality.checkM_method
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
102 #elif $filter.quality.source == 'genomeInfo'
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
103 --genomeInfo $filter.quality.genomeInfo
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
104 #elif $filter.quality.source == 'ignoreGenomeQuality'
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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105 --ignoreGenomeQuality
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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106 #end if
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
107 #end if
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
108 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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109
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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110 <xml name="genome_comparison_options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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111 <conditional name="genome_comparison">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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112 <param name="set_options" type="select" label="set genome comparison options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
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113 <option value="yes">Yes</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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114 <option value="no" selected="true">No</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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115 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
116 <when value="yes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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117 <param argument="--MASH_sketch" type="integer" value="1000" label="MASH sketch size"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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118 <param argument="--S_algorithm" type="select" label="Algorithm for secondary clustering comaprisons">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
119 <option value="ANImf" selected="true">ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
120 <option value="ANIn">ANIn = Align whole genomes with nucmer; compare aligned regions</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
121 <option value="gANI">gANI = Identify and align ORFs; compare aligned ORFS</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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122 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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123 <param argument="-n_PRESET" type="select" label="Presets to pass to nucmer">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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124 <option value="normal" selected="true">normal = default ANIn parameters (default: normal)</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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125 <option value="tight">tight = only align highly conserved regions</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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126 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
127 </when>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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128 <when value="no"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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129 </conditional>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
130 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
131 <token name="@GENOME_COMPARISON_OPTIONS@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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132 #if $genome_comparison.set_options == 'yes':
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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133 --MASH_sketch $genome_comparison.MASH_sketch
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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134 --S_algorithm $genome_comparison.S_algorithm
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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135 -n_PRESET $genome_comparison.n_PRESET
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
136 #end if
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
137 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
138
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
139 <xml name="clustering_options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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140 <conditional name="clustering">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
141 <param name="set_options" type="select" label="set clustering options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
142 <option value="yes">Yes</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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143 <option value="no" selected="true">No</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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144 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
145 <when value="yes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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146 <param argument="--P_ani" type="float" value="0.9" min="0." max="1." label="ANI threshold to form primary (MASH) clusters"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
147 <param argument="--S_ani" type="float" value="0.99" min="0." max="1." label="ANI threshold to form secondary clusters"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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148
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
149 <param argument="--SkipMash" type="boolean" truevalue="--SkipMash" falsevalue="" checked="false" label="Skip MASH clustering, just do secondary clustering on all genomes"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
150 <param argument="--SkipSecondary" type="boolean" truevalue="--SkipSecondary" falsevalue="" checked="false" label="Skip secondary clustering, just perform MASH clustering"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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diff changeset
151 <param argument="--cov_thresh" type="float" value="0.1" min="0." max="1." label="Minmum level of overlap between genomes when doing secondary comparisons"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
152 <param argument="--coverage_method" type="select" label="Method to calculate coverage of an alignment">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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153 <help>(for ANIn/ANImf only; gANI can only do larger method)</help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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154 <option value="larger" selected="true">arger = max((aligned length / genome 1), (aligned_length / genome2))</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
155 <option value="total">total = 2*(aligned length) / (sum of total genome lengths)</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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156 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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157 <param argument="--clusterAlg" type="select" label="Algorithm used to cluster genomes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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158 <help>(passed to scipy.cluster.hierarchy.linkage)</help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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diff changeset
159 <option value="average" selected="true">average</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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160 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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161 </when>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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162 <when value="no"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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163 </conditional>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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164 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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165 <token name="@CLUSTERING_OPTIONS@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
166 #if $clustering.set_options == 'yes':
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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167 --P_ani $clustering.P_ani
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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168 --S_ani $clustering.S_ani
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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169 $clustering.SkipMash
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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170 $clustering.SkipSecondary
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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171 --cov_thresh $clustering.cov_thresh
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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172 --coverage_method $clustering.coverage_method
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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173 --clusterAlg $clustering.clusterAlg
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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174 #end if
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
175 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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176
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
177 <xml name="scoring_options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
178 <conditional name="scoring">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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179 <param name="set_options" type="select" label="set scoring options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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180 <option value="yes">Yes</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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181 <option value="no" selected="true">No</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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182 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
183 <when value="yes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
184 <param argument="--completeness_weight" type="float" value="1" label="completeness weight">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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185 <help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
186 Based off of the formula:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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187 A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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188 A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight;
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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189 </help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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190 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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191 <param argument="--contamination_weight" type="float" value="5" label="contamination weight"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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192 <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="strain heterogeneity weight"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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193 <param argument="--N50_weight" type="float" value=".5" label="weight of log(genome N50)"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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194 <param argument="--size_weight" type="float" value="0" label="weight of log(genome size)"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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195 </when>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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196 <when value="no"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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197 </conditional>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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198 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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199 <token name="@SCORING_OPTIONS@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
200 #if $scoring.set_options == 'yes':
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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201 --completeness_weight $scoring.completeness_weight
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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202 --contamination_weight $scoring.contamination_weight
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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203 --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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204 --N50_weight $scoring.N50_weight
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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205 --size_weight $scoring.size_weight
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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206 #end if
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
207 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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208
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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209 <xml name="taxonomy_options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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210 <conditional name="taxonomy">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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211 <param name="set_options" type="select" label="generate taxonomy information">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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212 <option value="yes">Yes</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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213 <option value="no" selected="true">No</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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214 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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215 <when value="yes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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216 <param argument="--tax_method" type="select" label="Method of determining taxonomy">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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217 <help>(for ANIn/ANImf only; gANI can only do larger method)</help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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218 <option value="percent" selected="true">percent = The most descriptive taxonimic level with at least (per) hits</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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219 <option value="max">max = The centrifuge taxonomic level with the most overall hits</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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220 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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221 <param argument="--percent" type="float" value="50" min="0" max="100" label="minimum percent for percent method"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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222 <param argument="--cent_index" type="data" format="" label="centrifuge index"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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223 </when>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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224 <when value="no"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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225 </conditional>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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226 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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227 <token name="@TAXONOMY_OPTIONS@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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228 #if $taxonomy.set_options == 'yes':
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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229 --run_tax
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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230 --tax_method $taxonomy.tax_method
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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diff changeset
231 --percent $taxonomy.percent
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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232 --cent_index $taxonomy.cent_index
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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233 #end if
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
234 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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235
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
236 <xml name="warning_options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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diff changeset
237 <conditional name="warning">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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diff changeset
238 <param name="set_options" type="select" label="set warning options">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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239 <option value="yes">Yes</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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240 <option value="no" selected="true">No</option>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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241 </param>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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242 <when value="yes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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243 <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="How far from the threshold to throw cluster warnings"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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244 <param argument="--warn_sim" type="float" value="0.98" min="0" max="1" label="Similarity threshold for warnings between dereplicated genomes"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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diff changeset
245 <param argument="--warn_aln" type="float" value="0.25" min="0" max="1" label="Minimum aligned fraction for warnings between dereplicated genomes (ANIn)"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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246 </when>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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247 <when value="no"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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248 </conditional>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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249 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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250 <token name="@WARNING_OPTIONS@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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diff changeset
251 #if $warning.set_options == 'yes':
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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252 --warn_dist $warning.warn_dist
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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253 --warn_sim $warning.warn_sim
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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254 --warn_aln $warning.warn_aln
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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255 #end if
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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diff changeset
256 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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257
1
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
jjohnson
parents: 0
diff changeset
258 <xml name="select_outputs">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
jjohnson
parents: 0
diff changeset
259 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
jjohnson
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diff changeset
260 <option value="log" selected="true">log</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
jjohnson
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261 <option value="warnings" selected="true">Warnings</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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262 <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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263 <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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264 <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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265 <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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266 <yield/>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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267 </param>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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268 </xml>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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269 <xml name="select_drep_outputs">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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270 <expand macro="select_outputs">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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271 <option value="Cluster_scoring">Cluster_scoring.pdf</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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272 <option value="Winning_genomes">Winning_genomes.pdf</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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273 <option value="Widb">Widb.csv</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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274 <option value="Chdb">Chdb.tsv</option>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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275 </expand>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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276 </xml>
0
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277
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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278 <xml name="common_outputs">
1
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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279 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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280 <filter>'log' in select_outputs or not select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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281 </data>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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282 <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Warnings" from_work_dir="outdir/log/warnings.txt">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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283 <filter>'warnings' in select_outputs</filter>
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284 </data>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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285 <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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286 <filter>'Primary_clustering_dendrogram' in select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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287 </data>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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288 <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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289 <filter>'Secondary_clustering_dendrograms' in select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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290 </data>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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291 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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292 <filter>'Secondary_clustering_MDS' in select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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293 </data>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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294 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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295 <filter>'Clustering_scatterplots' in select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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296 </data>
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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297 </xml>
1
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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298
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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299
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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300 <xml name="drep_outputs">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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301 <expand macro="common_outputs"/>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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302 <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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303 <filter>'Cluster_scoring' in select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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304 </data>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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305 <data name="Winning_genomes" format="pdf" label="${tool.name} on ${on_string}: Winning_genomes.pdf" from_work_dir="outdir/figures/Winning_genomes.pdf">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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306 <filter>'Winning_genomes' in select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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307 </data>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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308 <data name="Widb" format="csv" label="${tool.name} on ${on_string}: Widb.csv" from_work_dir="outdir/data_tables/Widb.csv">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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309 <filter>'Widb' in select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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310 </data>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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311 <data name="Chdb" format="tabular" label="${tool.name} on ${on_string}: Chdb.tsv" from_work_dir="outdir/data/checkM/checkM_outdir/Chdb.tsv">
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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312 <filter>'Chdb' in select_outputs</filter>
7e2debc267eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
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313 </data>
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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314 </xml>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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315
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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316
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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317 <xml name="test_defaults_log">
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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318 <test>
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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319 <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/>
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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320 <output name="log">
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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321 <assert_contents>
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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322 <yield/>
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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323 </assert_contents>
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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324 </output>
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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325 </test>
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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326 </xml>
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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327
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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328 <token name="@GENOMES_HELP@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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329 I/O PARAMETERS:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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330 -g [GENOMES [GENOMES ...]], --genomes [GENOMES [GENOMES ...]]
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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331 genomes to cluster in .fasta format
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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332 (default: None)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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333
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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334
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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diff changeset
335 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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336
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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337 <token name="@FILTERING_HELP@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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338 FILTERING OPTIONS:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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339 -l LENGTH, --length LENGTH
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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340 Minimum genome length
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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341 (default: 50000)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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342
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
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343
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
344 -comp COMPLETENESS, --completeness COMPLETENESS
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
345 Minumum genome completeness
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
346 (default: 75)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
347
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
348
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
349 -con CONTAMINATION, --contamination CONTAMINATION
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
350 Maximum genome contamination
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
351 (default: 25)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
352
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
353
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
354 --ignoreGenomeQuality
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
355 Don't run checkM or do any quality filtering. NOT
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
356 RECOMMENDED! This is useful for use with
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
357 bacteriophages or eukaryotes or things where checkM
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
358 scoring does not work. Will only choose genomes based
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
359 on length and N50 (default: False)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
360
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
361
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
362 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
363
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
364 <token name="@GENOME_COMPARISON_HELP@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
365 GENOME COMPARISON PARAMETERS:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
366 -ms MASH_SKETCH, --MASH_sketch MASH_SKETCH
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
367 MASH sketch size (default: 1000)
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
368
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
369 --S_algorithm {goANI,ANIn,ANImf,gANI}
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
370 Algorithm for secondary clustering comaprisons:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
371 ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
372 ANIn = Align whole genomes with nucmer; compare aligned regions
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
373 gANI = Identify and align ORFs; compare aligned ORFS
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
374 (default: ANImf)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
375
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
376 -n_PRESET {normal,tight}
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
377 Presets to pass to nucmer
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
378 tight = only align highly conserved regions
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
379 normal = default ANIn parameters (default: normal)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
380
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
381 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
382
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
383 <token name="@CLUSTERING_HELP@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
384 CLUSTERING PARAMETERS:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
385 -pa P_ANI, --P_ani P_ANI
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
386 ANI threshold to form primary (MASH) clusters
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
387 (default: 0.9)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
388 -sa S_ANI, --S_ani S_ANI
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
389 ANI threshold to form secondary clusters
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
390 (default: 0.99)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
391
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
392 --SkipMash Skip MASH clustering, just do secondary clustering on
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
393 all genomes (default: False)
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
394 --SkipSecondary Skip secondary clustering, just perform MASH clustering
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
395 (default: False)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
396
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
397 -nc COV_THRESH, --cov_thresh COV_THRESH
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
398 Minmum level of overlap between genomes when doing
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
399 secondary comparisons (default: 0.1)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
400 -cm {total,larger}, --coverage_method {total,larger}
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
401 Method to calculate coverage of an alignment
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
402 (for ANIn/ANImf only; gANI can only do larger method)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
403 total = 2*(aligned length) / (sum of total genome lengths)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
404 larger = max((aligned length / genome 1), (aligned_length / genome2))
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
405 (default: larger)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
406
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
407 --clusterAlg CLUSTERALG
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
408 Algorithm used to cluster genomes (passed to
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
409 scipy.cluster.hierarchy.linkage (default: average)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
410
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
411 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
412
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
413 <token name="@SCORING_HELP@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
414 SCORING CRITERIA
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
415 Based off of the formula:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
416 A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
417
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
418 A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
419 -comW COMPLETENESS_WEIGHT, --completeness_weight COMPLETENESS_WEIGHT
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
420 completeness weight (default: 1)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
421 -conW CONTAMINATION_WEIGHT, --contamination_weight CONTAMINATION_WEIGHT
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
422 contamination weight (default: 5)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
423 -strW STRAIN_HETEROGENEITY_WEIGHT, --strain_heterogeneity_weight STRAIN_HETEROGENEITY_WEIGHT
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
424 strain heterogeneity weight (default: 1)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
425 -N50W N50_WEIGHT, --N50_weight N50_WEIGHT
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
426 weight of log(genome N50) (default: 0.5)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
427 -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
428 weight of log(genome size) (default: 0)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
429
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
430
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
431 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
432
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
433 <token name="@TAXONOMY_HELP@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
434 TAXONOMY:
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
435 --run_tax generate taxonomy information (Tdb)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
436 (default: False)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
437
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
438 --tax_method {percent,max}
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
439 Method of determining taxonomy
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
440 percent = The most descriptive taxonimic level with at least (per) hits
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
441 max = The centrifuge taxonomic level with the most overall hits
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
442 (default: percent)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
443
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
444
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
445 -per PERCENT, --percent PERCENT
2
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
446 minimum percent for percent method
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
447 (default: 50)
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
448
cb2fc9f60381 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
jjohnson
parents: 1
diff changeset
449
0
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
450 --cent_index CENT_INDEX
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
451 path to centrifuge index (for example,
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
452 /home/mattolm/download/centrifuge/indices/b+h+v
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
453 (default: None)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
454
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
455 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
456
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
457 <token name="@WARNINGS_HELP@"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
458 WARNINGS:
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
459 --warn_dist WARN_DIST
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
460 How far from the threshold to throw cluster warnings
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
461 (default: 0.25)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
462 --warn_sim WARN_SIM Similarity threshold for warnings between dereplicated
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
463 genomes (default: 0.98)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
464 --warn_aln WARN_ALN Minimum aligned fraction for warnings between
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
465 dereplicated genomes (ANIn) (default: 0.25)
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
466
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
467 ]]></token>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
468
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
469
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
parents:
diff changeset
470 </macros>