drep: macros.xml annotate

annotate macros.xml @ 0:cb142f79f424 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"

author	jjohnson
date	Mon, 06 Jan 2020 15:37:18 +0000
parents
children

rev	line source
0 cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	1 <macros>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	2 <token name="@VERSION@">2.3.2</token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	3 <xml name="requirements">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	4 <requirements>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	5 <requirement type="package" version="@VERSION@">drep</requirement>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	6 <yield/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	7 </requirements>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	8 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	9 <xml name="citations">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	10 <citations>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	11 <citation type="doi">10.1038/ismej.2017.126</citation>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	12 <yield />
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	13 </citations>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	14 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	15
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	16
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	17 <xml name="genomes">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	18 <param argument="--genomes" type="data" format="fasta" label="genomes fasta files" multiple="true"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	19 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	20 <token name="@PREPARE_GENOMES@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	21 #import re
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	22 #set $genomefiles = []
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	23 #for $genome in $genomes
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	24 #set $input_name = $re.sub('[^\w\-_.]', '_',str($genome.element_identifier.split('/')[-1]))
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	25 ln -s '${genome}' '${input_name}' &&
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	26 $genomefiles.append($input_name)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	27 #end for
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	28 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	29 <token name="@GENOMES@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	30 -g
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	31 #for $genomefile in $genomefiles
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	32 '${genomefile}'
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	33 #end for
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	34 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	35
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	36
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	37 <xml name="checkm_method">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	38 <param argument="--checkM_method" type="select" label="checkm method" optional="true">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	39 <option value="lineage_wf">lineage_wf (more accurate)</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	40 <option value="taxonomy_wf">taxonomy_wf (faster)</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	41 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	42 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	43 <token name="@CHECKM_METHOD@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	44 #if $checkM_method:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	45 --checkM_method $checkM_method
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	46 #end if
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	47 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	48
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	49 <xml name="filtering_options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	50 <conditional name="filter">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	51 <param name="set_options" type="select" label="set filtering options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	52 <option value="yes">Yes</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	53 <option value="no" selected="true">No</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	54 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	55 <when value="yes">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	56 <param argument="--length" type="integer" value="50000" label="Minimum genome length"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	57 <param argument="--completeness" type="integer" value="75" min="0" max="100" label="Minimum genome completeness percent"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	58 <param argument="--contamination" type="integer" value="25" min="0" max="100" label="Maximum genome contamination percent"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	59
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	60 <conditional name="quality">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	61 <param argument="source" type="select" label="genome quality">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	62 <help>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	63 --ignoreGenomeQuality is useful with
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	64 bacteriophages or eukaryotes or things where checkM
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	65 scoring does not work. Will only choose genomes based
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	66 on length and N50.
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	67 </help>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	68 <option value="checkm" selected="true">Run checkM</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	69 <option value="genomeInfo">User supplied genomeInfo csv file</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	70 <option value="ignoreGenomeQuality">--ignoreGenomeQuality (NOT RECOMMENDED!)</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	71 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	72 <when value="checkm">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	73 <param argument="--checkM_method" type="select" label="checkm method" optional="true">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	74 <option value="lineage_wf">lineage_wf (more accurate)</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	75 <option value="taxonomy_wf">taxonomy_wf (faster)</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	76 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	77 </when>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	78 <when value="genomeInfo">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	79 <param argument="--genomeInfo" type="data" format="csv" label="genomes fasta files">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	80 <help><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	81 A CSV dataset that must contain: [
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	82 "genome"(history dataset name of .fasta dataset of that genome),
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	83 "completeness"(0-100 value for completeness of the genome),
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	84 "contamination"(0-100 value of the contamination of the genome)]
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	85 ]]></help>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	86 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	87 </when>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	88 <when value="ignoreGenomeQuality"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	89 </conditional>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	90
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	91 </when>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	92 <when value="no"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	93 </conditional>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	94 </xml>
cb142f79f424 "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[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	96 #if $filter.set_options == 'yes':
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	97 --length $filter.length
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	98 --completeness $filter.completeness
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	99 --contamination $filter.contamination
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	100 #if $filter.quality.source == 'checkm'
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	101 --checkM_method $filter.quality.checkM_method
cb142f79f424 "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'
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	103 --genomeInfo $filter.quality.genomeInfo
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	104 #elif $filter.quality.source == 'ignoreGenomeQuality'
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	105 --ignoreGenomeQuality
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	106 #end if
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	107 #end if
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	108 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	109
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	110 <xml name="genome_comparison_options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	111 <conditional name="genome_comparison">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	112 <param name="set_options" type="select" label="set genome comparison options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	113 <option value="yes">Yes</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	114 <option value="no" selected="true">No</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	115 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	116 <when value="yes">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	117 <param argument="--MASH_sketch" type="integer" value="1000" label="MASH sketch size"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	118 <param argument="--S_algorithm" type="select" label="Algorithm for secondary clustering comaprisons">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	119 <option value="ANImf" selected="true">ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	120 <option value="ANIn">ANIn = Align whole genomes with nucmer; compare aligned regions</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	121 <option value="gANI">gANI = Identify and align ORFs; compare aligned ORFS</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	122 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	123 <param argument="-n_PRESET" type="select" label="Presets to pass to nucmer">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	124 <option value="normal" selected="true">normal = default ANIn parameters (default: normal)</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	125 <option value="tight">tight = only align highly conserved regions</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	126 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	127 </when>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	128 <when value="no"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	129 </conditional>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	130 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	131 <token name="@GENOME_COMPARISON_OPTIONS@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	132 #if $genome_comparison.set_options == 'yes':
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	133 --MASH_sketch $genome_comparison.MASH_sketch
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	134 --S_algorithm $genome_comparison.S_algorithm
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	135 -n_PRESET $genome_comparison.n_PRESET
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	136 #end if
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	137 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	138
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	139 <xml name="clustering_options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	140 <conditional name="clustering">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	141 <param name="set_options" type="select" label="set clustering options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	142 <option value="yes">Yes</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	143 <option value="no" selected="true">No</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	144 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	145 <when value="yes">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	146 <param argument="--P_ani" type="float" value="0.9" min="0." max="1." label="ANI threshold to form primary (MASH) clusters"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	147 <param argument="--S_ani" type="float" value="0.99" min="0." max="1." label="ANI threshold to form secondary clusters"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	148
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	149 <param argument="--SkipMash" type="boolean" truevalue="--SkipMash" falsevalue="" checked="false" label="Skip MASH clustering, just do secondary clustering on all genomes"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	150 <param argument="--SkipSecondary" type="boolean" truevalue="--SkipSecondary" falsevalue="" checked="false" label="Skip secondary clustering, just perform MASH clustering"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: 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"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	152 <param argument="--coverage_method" type="select" label="Method to calculate coverage of an alignment">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	153 <help>(for ANIn/ANImf only; gANI can only do larger method)</help>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	154 <option value="larger" selected="true">arger = max((aligned length / genome 1), (aligned_length / genome2))</option>
cb142f79f424 "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>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	156 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	157 <param argument="--clusterAlg" type="select" label="Algorithm used to cluster genomes">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	158 <help>(passed to scipy.cluster.hierarchy.linkage)</help>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	159 <option value="average" selected="true">average</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	160 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	161 </when>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	162 <when value="no"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	163 </conditional>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	164 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	165 <token name="@CLUSTERING_OPTIONS@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	166 #if $clustering.set_options == 'yes':
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	167 --P_ani $clustering.P_ani
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	168 --S_ani $clustering.S_ani
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	169 $clustering.SkipMash
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	170 $clustering.SkipSecondary
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	171 --cov_thresh $clustering.cov_thresh
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	172 --coverage_method $clustering.coverage_method
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	173 --clusterAlg $clustering.clusterAlg
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	174 #end if
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	175 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	176
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	177 <xml name="scoring_options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	178 <conditional name="scoring">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	179 <param name="set_options" type="select" label="set scoring options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	180 <option value="yes">Yes</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	181 <option value="no" selected="true">No</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	182 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	183 <when value="yes">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	184 <param argument="--completeness_weight" type="float" value="1" label="completeness weight">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	185 <help>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	186 Based off of the formula:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	187 ACompleteness - BContamination + C(Contamination (strain_heterogeneity/100)) + Dlog(N50) + Elog(size)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	188 A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight;
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	189 </help>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	190 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	191 <param argument="--contamination_weight" type="float" value="5" label="contamination weight"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	192 <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="strain heterogeneity weight"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	193 <param argument="--N50_weight" type="float" value=".5" label="weight of log(genome N50)"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	194 <param argument="--size_weight" type="float" value="0" label="weight of log(genome size)"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	195 </when>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	196 <when value="no"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	197 </conditional>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	198 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	199 <token name="@SCORING_OPTIONS@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	200 #if $scoring.set_options == 'yes':
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	201 --completeness_weight $scoring.completeness_weight
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	202 --contamination_weight $scoring.contamination_weight
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	203 --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	204 --N50_weight $scoring.N50_weight
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	205 --size_weight $scoring.size_weight
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	206 #end if
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	207 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	208
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	209 <xml name="taxonomy_options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	210 <conditional name="taxonomy">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	211 <param name="set_options" type="select" label="generate taxonomy information">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	212 <option value="yes">Yes</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	213 <option value="no" selected="true">No</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	214 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	215 <when value="yes">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	216 <param argument="--tax_method" type="select" label="Method of determining taxonomy">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	217 <help>(for ANIn/ANImf only; gANI can only do larger method)</help>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	218 <option value="percent" selected="true">percent = The most descriptive taxonimic level with at least (per) hits</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	219 <option value="max">max = The centrifuge taxonomic level with the most overall hits</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	220 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	221 <param argument="--percent" type="float" value="50" min="0" max="100" label="minimum percent for percent method"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	222 <param argument="--cent_index" type="data" format="" label="centrifuge index"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	223 </when>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	224 <when value="no"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	225 </conditional>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	226 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	227 <token name="@TAXONOMY_OPTIONS@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	228 #if $taxonomy.set_options == 'yes':
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	229 --run_tax
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	230 --tax_method $taxonomy.tax_method
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	231 --percent $taxonomy.percent
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	232 --cent_index $taxonomy.cent_index
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	233 #end if
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	234 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	235
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	236 <xml name="warning_options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	237 <conditional name="warning">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	238 <param name="set_options" type="select" label="set warning options">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	239 <option value="yes">Yes</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	240 <option value="no" selected="true">No</option>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	241 </param>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	242 <when value="yes">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	243 <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="How far from the threshold to throw cluster warnings"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	244 <param argument="--warn_sim" type="float" value="0.98" min="0" max="1" label="Similarity threshold for warnings between dereplicated genomes"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: 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)"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	246 </when>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	247 <when value="no"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	248 </conditional>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	249 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	250 <token name="@WARNING_OPTIONS@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	251 #if $warning.set_options == 'yes':
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	252 --warn_dist $warning.warn_dist
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	253 --warn_sim $warning.warn_sim
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	254 --warn_aln $warning.warn_aln
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	255 #end if
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	256 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	257
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	258 <xml name="select_outputs">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	259 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	260
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	261 <xml name="common_outputs">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	262 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	263 <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/warnings.txt"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	264 <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	265 <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	266 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	267 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf"/>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	268 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	269 <xml name="common_outputs2">
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	270 </xml>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	271
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	272 <token name="@GENOMES_HELP@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	273 I/O PARAMETERS:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	274 -g [GENOMES [GENOMES ...]], --genomes [GENOMES [GENOMES ...]]
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	275 genomes to cluster in .fasta format (default: None)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	276 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	277
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	278 <token name="@FILTERING_HELP@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	279 FILTERING OPTIONS:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	280 -l LENGTH, --length LENGTH
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	281 Minimum genome length (default: 50000)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	282 -comp COMPLETENESS, --completeness COMPLETENESS
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	283 Minumum genome completeness (default: 75)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	284 -con CONTAMINATION, --contamination CONTAMINATION
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	285 Maximum genome contamination (default: 25)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	286 --ignoreGenomeQuality
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	287 Don't run checkM or do any quality filtering. NOT
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	288 RECOMMENDED! This is useful for use with
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	289 bacteriophages or eukaryotes or things where checkM
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	290 scoring does not work. Will only choose genomes based
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	291 on length and N50 (default: False)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	292
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	293
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	294 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	295
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	296 <token name="@GENOME_COMPARISON_HELP@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	297 GENOME COMPARISON PARAMETERS:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	298 -ms MASH_SKETCH, --MASH_sketch MASH_SKETCH
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	299 MASH sketch size (default: 1000)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	300 --S_algorithm {goANI,ANIn,ANImf,gANI}
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	301 Algorithm for secondary clustering comaprisons:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	302 ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	303 ANIn = Align whole genomes with nucmer; compare aligned regions
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	304 gANI = Identify and align ORFs; compare aligned ORFS
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	305 (default: ANImf)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	306 -n_PRESET {normal,tight}
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	307 Presets to pass to nucmer
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	308 tight = only align highly conserved regions
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	309 normal = default ANIn parameters (default: normal)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	310
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	311 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	312
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	313 <token name="@CLUSTERING_HELP@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	314 CLUSTERING PARAMETERS:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	315 -pa P_ANI, --P_ani P_ANI
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	316 ANI threshold to form primary (MASH) clusters
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	317 (default: 0.9)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	318 -sa S_ANI, --S_ani S_ANI
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	319 ANI threshold to form secondary clusters (default:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	320 0.99)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	321 --SkipMash Skip MASH clustering, just do secondary clustering on
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	322 all genomes (default: False)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	323 --SkipSecondary Skip secondary clustering, just perform MASH
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	324 clustering (default: False)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	325 -nc COV_THRESH, --cov_thresh COV_THRESH
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	326 Minmum level of overlap between genomes when doing
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	327 secondary comparisons (default: 0.1)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	328 -cm {total,larger}, --coverage_method {total,larger}
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	329 Method to calculate coverage of an alignment
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	330 (for ANIn/ANImf only; gANI can only do larger method)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	331 total = 2*(aligned length) / (sum of total genome lengths)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	332 larger = max((aligned length / genome 1), (aligned_length / genome2))
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	333 (default: larger)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	334 --clusterAlg CLUSTERALG
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	335 Algorithm used to cluster genomes (passed to
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	336 scipy.cluster.hierarchy.linkage (default: average)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	337
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	338 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	339
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	340 <token name="@SCORING_HELP@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	341 SCORING CRITERIA
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	342 Based off of the formula:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	343 ACompleteness - BContamination + C(Contamination (strain_heterogeneity/100)) + Dlog(N50) + Elog(size)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	344
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	345 A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	346 -comW COMPLETENESS_WEIGHT, --completeness_weight COMPLETENESS_WEIGHT
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	347 completeness weight (default: 1)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	348 -conW CONTAMINATION_WEIGHT, --contamination_weight CONTAMINATION_WEIGHT
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	349 contamination weight (default: 5)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	350 -strW STRAIN_HETEROGENEITY_WEIGHT, --strain_heterogeneity_weight STRAIN_HETEROGENEITY_WEIGHT
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	351 strain heterogeneity weight (default: 1)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	352 -N50W N50_WEIGHT, --N50_weight N50_WEIGHT
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	353 weight of log(genome N50) (default: 0.5)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	354 -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	355 weight of log(genome size) (default: 0)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	356
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	357 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	358
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	359 <token name="@TAXONOMY_HELP@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	360 TAXONOMY:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	361 --run_tax generate taxonomy information (Tdb) (default: False)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	362 --tax_method {percent,max}
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	363 Method of determining taxonomy
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	364 percent = The most descriptive taxonimic level with at least (per) hits
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	365 max = The centrifuge taxonomic level with the most overall hits (default: percent)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	366 -per PERCENT, --percent PERCENT
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	367 minimum percent for percent method (default: 50)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	368 --cent_index CENT_INDEX
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	369 path to centrifuge index (for example,
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	370 /home/mattolm/download/centrifuge/indices/b+h+v
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	371 (default: None)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	372
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	373 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	374
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	375 <token name="@WARNINGS_HELP@"><![CDATA[
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	376 WARNINGS:
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	377 --warn_dist WARN_DIST
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	378 How far from the threshold to throw cluster warnings
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	379 (default: 0.25)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	380 --warn_sim WARN_SIM Similarity threshold for warnings between dereplicated
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	381 genomes (default: 0.98)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	382 --warn_aln WARN_ALN Minimum aligned fraction for warnings between
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	383 dereplicated genomes (ANIn) (default: 0.25)
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	384
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	385 ]]></token>
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	386
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	387
cb142f79f424 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539" jjohnson parents: diff changeset	388 </macros>

Mercurial > repos > jjohnson > drep

annotate macros.xml @ 0:cb142f79f424 draft default tip