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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
author jjohnson
date Mon, 06 Jan 2020 11:11:06 -0500
parents
children 7e2debc267eb
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b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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1 <tool id="drep_dereplicate" name="dRep dereplicate" version="@VERSION@.0" python_template_version="3.5">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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2 <description>De-replicate a list of genomes</description>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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3 <macros>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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4 <import>macros.xml</import>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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5 </macros>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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6 <expand macro="requirements" />
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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7 <command detect_errors="exit_code"><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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8 @PREPARE_GENOMES@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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9 dRep dereplicate outdir
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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10 @FILTER_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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11 @GENOME_COMPARISON_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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12 @CLUSTERING_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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13 @SCORING_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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14 @TAXONOMY_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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15 @WARNING_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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16 @GENOMES@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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17 ]]></command>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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18 <inputs>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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19 <expand macro="genomes"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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20 <expand macro="filtering_options"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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21 <expand macro="genome_comparison_options"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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22 <expand macro="clustering_options"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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23 <expand macro="scoring_options"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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24 <expand macro="taxonomy_options"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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25 <expand macro="warning_options"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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26 </inputs>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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27 <outputs>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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28 <expand macro="common_outputs" />
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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29 <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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30 <discover_datasets pattern="__designation__" directory="out_drep/dereplicated_genomes" ext='fasta'/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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31 </collection>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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32 </outputs>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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33 <help><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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34 TODO: Fill in help.
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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35
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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36 usage: drep dereplicate [-p PROCESSORS] [-d] [-h] [-l LENGTH]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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37 [-comp COMPLETENESS] [-con CONTAMINATION]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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38 [--ignoreGenomeQuality] [-ms MASH_SKETCH]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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39 [--S_algorithm {goANI,ANIn,ANImf,gANI}]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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40 [-n_PRESET {normal,tight}] [-pa P_ANI] [-sa S_ANI]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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41 [--SkipMash] [--SkipSecondary] [-nc COV_THRESH]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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42 [-cm {total,larger}] [--clusterAlg CLUSTERALG]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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43 [-comW COMPLETENESS_WEIGHT]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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44 [-conW CONTAMINATION_WEIGHT]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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45 [-strW STRAIN_HETEROGENEITY_WEIGHT] [-N50W N50_WEIGHT]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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46 [-sizeW SIZE_WEIGHT] [--run_tax]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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47 [--tax_method {percent,max}] [-per PERCENT]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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48 [--cent_index CENT_INDEX] [--warn_dist WARN_DIST]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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49 [--warn_sim WARN_SIM] [--warn_aln WARN_ALN]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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50 [-g [GENOMES [GENOMES ...]]]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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51 [--checkM_method {taxonomy_wf,lineage_wf}]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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52 [--genomeInfo GENOMEINFO]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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53 work_directory
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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54
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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55 @GENOMES_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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56 @FILTERING_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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57 @GENOME_COMPARISON_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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58 @CLUSTERING_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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59 @SCORING_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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60 @TAXONOMY_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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61 @WARNINGS_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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62
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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63
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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64 ]]></help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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65 <expand macro="citations" />
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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66 </tool>