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annotate drep_compare.xml @ 0:b59ae99e47d4 draft

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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_compare" name="dRep compare" 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>compare 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 compare outdir
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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10 @GENOME_COMPARISON_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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11 @CLUSTERING_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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12 @TAXONOMY_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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13 @WARNING_OPTIONS@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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14 @GENOMES@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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15 ]]></command>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
jjohnson
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16 <inputs>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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17 <expand macro="genomes"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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18 <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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19 <expand macro="clustering_options"/>
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="taxonomy_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="warning_options"/>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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22 </inputs>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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23 <outputs>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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24 <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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25 <!--
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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26 outdir/data_tables/Cdb.csv
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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27 outdir/data_tables/Mdb.csv
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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28 outdir/data_tables/Ndb.csv
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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29 outdir/data_tables/Bdb.csv
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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30
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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31 <data name="foldChange" format="tabular" label="${tool.name} on ${on_string}: BayesianFoldChangeAnalysis.tsv" from_work_dir="out/BayesianFoldChangeAnalysis.tsv">
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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32 <filter>'bayesian' in experiment and 'ctr' in experiment['bayesian']</filter>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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33 </data>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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34 -->
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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35 </outputs>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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36 <help><![CDATA[
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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37 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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38
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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39 usage: drep compare [-p PROCESSORS] [-d] [-h] [-ms MASH_SKETCH]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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40 [--S_algorithm {ANIn,goANI,ANImf,gANI}]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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41 [-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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42 [--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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43 [-cm {total,larger}] [--clusterAlg CLUSTERALG] [--run_tax]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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44 [--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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45 [--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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46 [--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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47 [-g [GENOMES [GENOMES ...]]]
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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48 work_directory
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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49
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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50
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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51 @GENOMES_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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52 @GENOME_COMPARISON_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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53 @CLUSTERING_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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54 @TAXONOMY_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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55 @WARNINGS_HELP@
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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56
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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57 ]]></help>
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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58 <expand macro="citations" />
b59ae99e47d4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
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59 </tool>