Mercurial > repos > jjohnson > drep
comparison drep_compare.xml @ 0:b59ae99e47d4 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
author | jjohnson |
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date | Mon, 06 Jan 2020 11:11:06 -0500 |
parents | |
children | 7e2debc267eb |
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-1:000000000000 | 0:b59ae99e47d4 |
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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> |