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comparison 1.0.0/lib/help/gsrpy.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 gen_salmon_res_table.py (gsrpy) within CPIPES.
2
3 def gsrpyHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'gsrpy_run': [
12 clihelp: 'Run the gen_salmon_res_table.py script. Default: ' +
13 (params.gsrpy_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'gsrpy_url': [
18 clihelp: 'Generate an additional column in final results table ' +
19 'which links out to NCBI Pathogens Isolate Browser. ' +
20 " Default: ${params.gsrpy_url}",
21 cliflag: '-url',
22 clivalue: (params.gsrpy_url ? ' ' : '')
23 ]
24 ]
25
26 toolspecs.each {
27 k, v -> tool.text['--' + k] = "${v.clihelp}"
28 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
29 }
30
31 return tool
32 }