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comparison 0.7.0/lib/help/wcomp.nf @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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16:b90e5a7a3d4f 17:0e7a0053e4a6
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_seronamecol': [
19 clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
20 'name is "serovar". ' +
21 " Default: ${params.wcomp_seronamecol}",
22 cliflag: '--seronamecol',
23 clivalue: (params.wcomp_seronamecol ?: '')
24 ],
25 'wcomp_acc_col': [
26 clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
27 'name is "acc". ' +
28 " Default: ${params.wcomp_seronamecol}",
29 cliflag: '--acc_col',
30 clivalue: (params.wcomp_acc_col ?: '')
31 ],
32 'wcomp_target_acc_col': [
33 clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
34 'name is "target_acc". ' +
35 " Default: ${params.wcomp_seronamecol}",
36 cliflag: '--target_acc_col',
37 clivalue: (params.wcomp_target_acc_col ?: '')
38 ],
39 'wcomp_complete_sero': [
40 clihelp: 'Skip indexing serotypes when the serotype name in the column ' +
41 'number 49 (non 0-based) of PDG metadata file consists a "-". For example, if ' +
42 'an accession has a serotype= string as such in column ' +
43 'number 49 (non 0-based): ' +
44 '"serotype=- 13:z4,z23:-" ' +
45 'then, the indexing of that accession is skipped.' +
46 " Default: ${params.wcomp_complete_sero}",
47 cliflag: '--complete_serotype_name',
48 clivalue: (params.wcomp_complete_sero ? ' ' : '')
49 ],
50 'wcomp_not_null_serovar': [
51 clihelp: 'Only index the computed_serotype column ' +
52 'i.e. column number 49 (non 0-based), if the serovar column' +
53 ' is not NULL. ' +
54 " Default: ${params.wcomp_not_null_serovar}",
55 cliflag: '--not_null_serotype_name',
56 clivalue: (params.wcomp_not_null_serovar ?: '')
57 ],
58 'wcomp_i': [
59 clihelp: 'Force include this serovar. Ignores ' +
60 '--wcomp_complete_sero for only this serovar. ' +
61 'Mention multiple serovars separated by a ! (Exclamation mark). ' +
62 'Ex: --wcomp_complete_sero I 4,[5],12:i:-!Agona' +
63 " Default: ${params.wcomp_i}",
64 cliflag: '-i',
65 clivalue: (params.wcomp_i ? params.wcomp_i.split(/\!/).join(' -i ').trim().replace(/^\-i\s+/, '') : '')
66 ],
67 'wcomp_num': [
68 clihelp: 'Number of genome accessions to be collected per serotype.' +
69 " Default: ${params.wcomp_num}",
70 cliflag: '-num',
71 clivalue: (params.wcomp_num ?: '')
72 ],
73 'wcomp_min_contig_size': [
74 clihelp: 'Minimum contig size to consider a genome for indexing.' +
75 " Default: ${params.wcomp_min_contig_size}",
76 cliflag: '--min_contig_size',
77 clivalue: (params.wcomp_min_contig_size ?: '')
78 ]
79 ]
80
81 toolspecs.each {
82 k, v -> tool.text['--' + k] = "${v.clihelp}"
83 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
84 }
85
86 return tool
87 }