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comparison 0.5.0/lib/help/sourmashgather.nf @ 0:97cd2f532efe

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author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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-1:000000000000 0:97cd2f532efe
1 // Help text for sourmash gather within CPIPES.mashsketch
2
3 def sourmashgatherHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'sourmashgather_run': [
12 clihelp: 'Run `sourmash gather` tool. Default: ' +
13 (params.sourmashgather_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'sourmashgather_n': [
18 clihelp: 'Number of results to report. ' +
19 'By default, will terminate at --sourmashgather_thr_bp value. ' +
20 "Default: ${params.sourmashgather_n}",
21 cliflag: '-n',
22 clivalue: (params.sourmashgather_n ?: '')
23 ],
24 'sourmashgather_thr_bp': [
25 clihelp: 'Reporting threshold (in bp) for estimated overlap with remaining query. ' +
26 "Default: ${params.sourmashgather_thr_bp}",
27 cliflag: '--threshold-bp',
28 clivalue: (params.sourmashgather_thr_bp ?: '')
29 ],
30 'sourmashgather_ani_ci': [
31 clihelp: 'Output confidence intervals for ANI estimates. ' +
32 "Default: ${params.sourmashgather_ani_ci}",
33 cliflag: '--estimate-ani-ci',
34 clivalue: (params.sourmashgather_ani_ci ? ' ' : '')
35 ],
36 'sourmashgather_k': [
37 clihelp: 'The k-mer size to select. ' +
38 "Default: ${params.sourmashgather_k}",
39 cliflag: '-k',
40 clivalue: (params.sourmashgather_k ?: '')
41 ],
42 'sourmashgather_dna': [
43 clihelp: 'Choose DNA signature. ' +
44 "Default: ${params.sourmashgather_dna}",
45 cliflag: '--dna',
46 clivalue: (params.sourmashgather_dna ? ' ' : '')
47 ],
48 'sourmashgather_rna': [
49 clihelp: 'Choose RNA signature. ' +
50 "Default: ${params.sourmashgather_rna}",
51 cliflag: '--rna',
52 clivalue: (params.sourmashgather_rna ? ' ' : '')
53 ],
54 'sourmashgather_nuc': [
55 clihelp: 'Choose Nucleotide signature. ' +
56 "Default: ${params.sourmashgather_nuc}",
57 cliflag: '--nucleotide',
58 clivalue: (params.sourmashgather_nuc ? ' ' : '')
59 ],
60 'sourmashgather_scaled': [
61 clihelp: 'Scaled value should be between 100 and 1e6. ' +
62 "Default: ${params.sourmashgather_scaled}",
63 cliflag: '--scaled',
64 clivalue: (params.sourmashgather_scaled ?: '')
65 ],
66 'sourmashgather_inc_pat': [
67 clihelp: 'Search only signatures that match this pattern in name, filename, or md5. ' +
68 "Default: ${params.sourmashgather_inc_pat}",
69 cliflag: '--include-db-pattern',
70 clivalue: (params.sourmashgather_inc_pat ?: '')
71 ],
72 'sourmashgather_exc_pat': [
73 clihelp: 'Search only signatures that do not match this pattern in name, filename, or md5. ' +
74 "Default: ${params.sourmashgather_exc_pat}",
75 cliflag: '--exclude-db-pattern',
76 clivalue: (params.sourmashgather_exc_pat ?: '')
77 ]
78 ]
79
80 toolspecs.each {
81 k, v -> tool.text['--' + k] = "${v.clihelp}"
82 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
83 }
84
85 return tool
86 }