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comparison 1.0.0/lib/help/wsnp.nf @ 0:0a8dda29956e draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 // Help text for waterfall_per_snp_cluster.pl (wsnp) within CPIPES.
2
3 def wsnpHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'wsnp_serocol': [
12 clihelp: 'Column number (non 0-based index) of the PDG metadata file ' +
13 'by which the serotypes are collected.' +
14 " Default: ${params.wsnp_serocol}",
15 cliflag: '--serocol',
16 clivalue: (params.wsnp_serocol ?: '')
17 ],
18 'wsnp_seronamecol': [
19 clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
20 'name is "serovar". ' +
21 " Default: ${params.wsnp_seronamecol}",
22 cliflag: '--seronamecol',
23 clivalue: (params.wsnp_seronamecol ?: '')
24 ],
25 'wsnp_acc_col': [
26 clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
27 'name is "acc". ' +
28 " Default: ${params.wsnp_seronamecol}",
29 cliflag: '--acc_col',
30 clivalue: (params.wsnp_acc_col ?: '')
31 ],
32 'wsnp_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.wsnp_seronamecol}",
36 cliflag: '--target_acc_col',
37 clivalue: (params.wsnp_target_acc_col ?: '')
38 ],
39 'wsnp_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.wsnp_complete_sero}",
47 cliflag: '--complete_serotype_name',
48 clivalue: (params.wsnp_complete_sero ? ' ' : '')
49 ],
50 'wsnp_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.wsnp_not_null_serovar}",
55 cliflag: '--not_null_serotype_name',
56 clivalue: (params.wsnp_not_null_serovar ?: '')
57 ],
58 'wsnp_i': [
59 clihelp: 'Force include this serovar. Ignores ' +
60 '--wsnp_complete_sero for only this serovar. ' +
61 'Mention multiple serovars separated by a ! (Exclamation mark). ' +
62 'Ex: --wsnp_complete_sero I 4,[5],12:i:-!Agona' +
63 " Default: ${params.wsnp_i}",
64 cliflag: '-i',
65 clivalue: (params.wsnp_i ? params.wsnp_i.split(/\!/).join(' -i ').trim().replace(/^\-i\s+/, '') : '')
66 ],
67 'wsnp_num': [
68 clihelp: 'Number of genome accessions to collect per SNP cluster.' +
69 " Default: ${params.wsnp_num}",
70 cliflag: '-num',
71 clivalue: (params.wsnp_num ?: '')
72 ]
73 ]
74
75 toolspecs.each {
76 k, v -> tool.text['--' + k] = "${v.clihelp}"
77 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
78 }
79
80 return tool
81 }