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comparison 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
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children 7e2debc267eb
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-1:000000000000 0:b59ae99e47d4
1 <tool id="drep_compare" name="dRep compare" version="@VERSION@.0" python_template_version="3.5">
2 <description>compare a list of genomes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 @PREPARE_GENOMES@
9 dRep compare outdir
10 @GENOME_COMPARISON_OPTIONS@
11 @CLUSTERING_OPTIONS@
12 @TAXONOMY_OPTIONS@
13 @WARNING_OPTIONS@
14 @GENOMES@
15 ]]></command>
16 <inputs>
17 <expand macro="genomes"/>
18 <expand macro="genome_comparison_options"/>
19 <expand macro="clustering_options"/>
20 <expand macro="taxonomy_options"/>
21 <expand macro="warning_options"/>
22 </inputs>
23 <outputs>
24 <expand macro="common_outputs" />
25 <!--
26 outdir/data_tables/Cdb.csv
27 outdir/data_tables/Mdb.csv
28 outdir/data_tables/Ndb.csv
29 outdir/data_tables/Bdb.csv
30
31 <data name="foldChange" format="tabular" label="${tool.name} on ${on_string}: BayesianFoldChangeAnalysis.tsv" from_work_dir="out/BayesianFoldChangeAnalysis.tsv">
32 <filter>'bayesian' in experiment and 'ctr' in experiment['bayesian']</filter>
33 </data>
34 -->
35 </outputs>
36 <help><![CDATA[
37 TODO: Fill in help.
38
39 usage: drep compare [-p PROCESSORS] [-d] [-h] [-ms MASH_SKETCH]
40 [--S_algorithm {ANIn,goANI,ANImf,gANI}]
41 [-n_PRESET {normal,tight}] [-pa P_ANI] [-sa S_ANI]
42 [--SkipMash] [--SkipSecondary] [-nc COV_THRESH]
43 [-cm {total,larger}] [--clusterAlg CLUSTERALG] [--run_tax]
44 [--tax_method {percent,max}] [-per PERCENT]
45 [--cent_index CENT_INDEX] [--warn_dist WARN_DIST]
46 [--warn_sim WARN_SIM] [--warn_aln WARN_ALN]
47 [-g [GENOMES [GENOMES ...]]]
48 work_directory
49
50
51 @GENOMES_HELP@
52 @GENOME_COMPARISON_HELP@
53 @CLUSTERING_HELP@
54 @TAXONOMY_HELP@
55 @WARNINGS_HELP@
56
57 ]]></help>
58 <expand macro="citations" />
59 </tool>