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comparison 1.0.0/lib/help/sfhpy.nf @ 0:801b85b03a17 draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 // Help text for sourmash_filter_hits.py (sfhpy) within CPIPES.
2 def sfhpyHelp(params) {
3
4 Map tool = [:]
5 Map toolspecs = [:]
6 tool.text = [:]
7 tool.helpparams = [:]
8
9 toolspecs = [
10 'sfhpy_run': [
11 clihelp: 'Run the sourmash_filter_hits.py ' +
12 'script. Default: ' +
13 (params.sfhpy_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'sfhpy_fcn': [
18 clihelp: 'Column name by which filtering of rows should be applied. ' +
19 "Default: ${params.sfhpy_fcn}",
20 cliflag: '-fcn',
21 clivalue: (params.sfhpy_fcn ?: '')
22 ],
23 'sfhpy_fcv': [
24 clihelp: 'Remove genomes whose match with the query FASTQ is less than ' +
25 'this much. ' +
26 "Default: ${params.sfhpy_fcv}",
27 cliflag: '-fcv',
28 clivalue: (params.sfhpy_fcv ?: '')
29 ],
30 'sfhpy_gt': [
31 clihelp: 'Apply greather than or equal to condition on numeric values of ' +
32 '--sfhpy_fcn column. ' +
33 "Default: ${params.sfhpy_gt}",
34 cliflag: '-gt',
35 clivalue: (params.sfhpy_gt ? ' ' : '')
36 ],
37 'sfhpy_lt': [
38 clihelp: 'Apply less than or equal to condition on numeric values of ' +
39 '--sfhpy_fcn column. ' +
40 "Default: ${params.sfhpy_lt}",
41 cliflag: '-gt',
42 clivalue: (params.sfhpy_lt ? ' ' : '')
43 ],
44 ]
45
46 toolspecs.each {
47 k, v -> tool.text['--' + k] = "${v.clihelp}"
48 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
49 }
50
51 return tool
52 }