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comparison 0.5.0/lib/help/wcomp.nf @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 // Help text for waterfall_per_computed_serotype.pl (wcomp) within CPIPES.
2
3 def wcompHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'wcomp_serocol': [
12 clihelp: 'Column number (non 0-based index) of the PDG metadata file ' +
13 'by which the serotypes are collected.' +
14 " Default: ${params.wcomp_serocol}",
15 cliflag: '--serocol',
16 clivalue: (params.wcomp_serocol ?: '')
17 ],
18 'wcomp_complete_sero': [
19 clihelp: 'Skip indexing serotypes when the serotype name in the column ' +
20 'number 49 (non 0-based) of PDG metadata file consists a "-". For example, if ' +
21 'an accession has a serotype= string as such in column ' +
22 'number 49 (non 0-based): ' +
23 '"serotype=- 13:z4,z23:-" ' +
24 'then, the indexing of that accession is skipped.' +
25 " Default: ${params.wcomp_complete_sero}",
26 cliflag: '--complete_serotype_name',
27 clivalue: (params.wcomp_complete_sero ? ' ' : '')
28 ],
29 'wcomp_not_null_serovar': [
30 clihelp: 'Only index the computed_serotype column ' +
31 'i.e. column number 49 (non 0-based), if the serovar column' +
32 ' is not NULL. ' +
33 " Default: ${params.wcomp_not_null_serovar}",
34 cliflag: '--not_null_serotype_name',
35 clivalue: (params.wcomp_not_null_serovar ?: '')
36 ],
37 'wcomp_i': [
38 clihelp: 'Force include this serovar. Ignores ' +
39 '--wcomp_complete_sero for only this serovar. ' +
40 'Mention multiple serovars separated by a ! (Exclamation mark). ' +
41 'Ex: --wcomp_complete_sero I 4,[5],12:i:-!Agona' +
42 " Default: ${params.wcomp_i}",
43 cliflag: '-i',
44 clivalue: (params.wcomp_i ? params.wcomp_i.split(/\!/).join(' -i ').trim().replace(/^\-i\s+/, '') : '')
45 ],
46 'wcomp_num': [
47 clihelp: 'Number of genome accessions to be collected per serotype.' +
48 " Default: ${params.wcomp_num}",
49 cliflag: '-num',
50 clivalue: (params.wcomp_num ?: '')
51 ],
52 'wcomp_min_contig_size': [
53 clihelp: 'Minimum contig size to consider a genome for indexing.' +
54 " Default: ${params.wcomp_min_contig_size}",
55 cliflag: '--min_contig_size',
56 clivalue: (params.wcomp_min_contig_size ?: '')
57 ]
58 ]
59
60 toolspecs.each {
61 k, v -> tool.text['--' + k] = "${v.clihelp}"
62 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
63 }
64
65 return tool
66 }