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comparison 0.2.0/lib/help/mashtree.nf @ 0:9e8b1c747a6a draft default tip

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author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 // Help text for mashtree within CPIPES.
2
3 def mashtreeHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'mashtree_run': [
12 clihelp: 'Run mashtree tool. Default: ' +
13 (params.mashtree_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'mashtree_fofn': [
18 clihelp: 'Input is a file of file names. ' +
19 "Default: ${params.mashtree_fofn}",
20 cliflag: '--file-of-files',
21 clivalue: (params.mashtree_fofn ? ' ' : '')
22 ],
23 'mashtree_trunclength': [
24 clihelp: 'How many characters to keep in filename. ' +
25 "Default: ${params.mashtree_trunclength}",
26 cliflag: '--truncLength',
27 clivalue: (params.mashtree_trunclength ?: '')
28 ],
29 'mashtree_mindepth': [
30 clihelp: 'If mindepth is zero, then it will be chosen in a smart but slower method, ' +
31 'to discard lower-abundance kmers. ' +
32 "Default: ${params.mashtree_mindepth}",
33 cliflag: '--mindepth',
34 clivalue: (params.mashtree_mindepth ?: '')
35 ],
36 'mashtree_kmerlength': [
37 clihelp: "The minimum k-mer length. " +
38 "Default: ${params.mashtree_kmerlength}",
39 cliflag: '--kmerlength',
40 clivalue: (params.mashtree_kmerlength ?: '')
41 ],
42 'mashtree_sketchsize': [
43 clihelp: "The minimum `mash` sketch size. " +
44 "Default: ${params.mashtree_sketchsize}",
45 cliflag: '--sketchsize',
46 clivalue: (params.mashtree_sketchsize ?: '')
47 ],
48 'mashtree_seed': [
49 clihelp: "Seed for `mash` sketch. " +
50 "Default: ${params.mashtree_seed}",
51 cliflag: '--seed',
52 clivalue: (params.mashtree_seed ? ' ' : '')
53 ],
54 'mashtree_genomesize': [
55 clihelp: 'Define genome size. ' +
56 "Default: ${params.mashtree_genomesize}",
57 cliflag: '--genomesize',
58 clivalue: (params.mashtree_genomesize ?: '')
59 ],
60 'mashtree_sigfigs': [
61 clihelp: "How many decimal places to use in mash distances. " +
62 "Default: ${params.mashtree_sigfigs}",
63 cliflag: '--sigfigs',
64 clivalue: (params.mashtree_sigfigs ?: '')
65 ],
66 'mashtree_sortorder': [
67 clihelp: 'For neighbor-joining, the sort order can make a difference. ' +
68 'Options include: ABC (alphabetical), random, input-order. ' +
69 "Default: ${params.mashtree_sortorder}",
70 cliflag: '--sort-order',
71 clivalue: (params.mashtree_sortorder ?: '')
72 ]
73 ]
74
75 toolspecs.each {
76 k, v -> tool.text['--' + k] = "${v.clihelp}"
77 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
78 }
79
80 return tool
81 }