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comparison 0.5.0/lib/help/gsalkronapy.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 `gen_salmon_tph_and_krona_tsv.py` (gsalkronapy) within CPIPES.
2
3 def gsalkronapyHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'gsalkronapy_run': [
12 clihelp: 'Run the `gen_salmon_tph_and_krona_tsv.py` script. Default: ' +
13 (params.gsalkronapy_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'gsalkronapy_sf': [
18 clihelp: 'Set the scaling factor by which TPM values ' +
19 'are scaled down.' +
20 " Default: ${params.gsalkronapy_sf}",
21 cliflag: '-sf',
22 clivalue: (params.gsalkronapy_sf ?: '')
23 ],
24 'gsalkronapy_smres_suffix': [
25 clihelp: 'Find the `sourmash gather` result files ' +
26 'ending in this suffix.' +
27 " Default: ${params.gsalkronapy_smres_suffix}",
28 cliflag: '-smres-suffix',
29 clivalue: (params.gsalkronapy_smres_suffix ?: '')
30 ],
31 'gsalkronapy_failed_suffix': [
32 clihelp: 'Find the sample names which failed classification stored ' +
33 'inside the files ending in this suffix.' +
34 " Default: ${params.gsalkronapy_failed_suffix}",
35 cliflag: '-failed-suffix',
36 clivalue: (params.gsalkronapy_failed_suffix ?: '')
37 ],
38 'gsalkronapy_num_lin_cols': [
39 clihelp: 'Number of columns expected in the lineages CSV file. ' +
40 " Default: ${params.gsalkronapy_num_lin_cols}",
41 cliflag: '-num-lin-cols',
42 clivalue: (params.gsalkronapy_num_lin_cols ?: '')
43 ],
44 'gsalkronapy_lin_regex': [
45 clihelp: 'Number of columns expected in the lineages CSV file. ' +
46 " Default: ${params.gsalkronapy_num_lin_cols}",
47 cliflag: '-num-lin-cols',
48 clivalue: (params.gsalkronapy_num_lin_cols ?: '')
49 ]
50 ]
51
52 toolspecs.each {
53 k, v -> tool.text['--' + k] = "${v.clihelp}"
54 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
55 }
56
57 return tool
58 }