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annotate 0.6.1/lib/help/gsrpy.nf @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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kkonganti@11 1 // Help text for gen_salmon_res_table.py (gsrpy) within CPIPES.
kkonganti@11 2
kkonganti@11 3 def gsrpyHelp(params) {
kkonganti@11 4
kkonganti@11 5 Map tool = [:]
kkonganti@11 6 Map toolspecs = [:]
kkonganti@11 7 tool.text = [:]
kkonganti@11 8 tool.helpparams = [:]
kkonganti@11 9
kkonganti@11 10 toolspecs = [
kkonganti@11 11 'gsrpy_run': [
kkonganti@11 12 clihelp: 'Run the gen_salmon_res_table.py script. Default: ' +
kkonganti@11 13 (params.gsrpy_run ?: false),
kkonganti@11 14 cliflag: null,
kkonganti@11 15 clivalue: null
kkonganti@11 16 ],
kkonganti@11 17 'gsrpy_url': [
kkonganti@11 18 clihelp: 'Generate an additional column in final results table ' +
kkonganti@11 19 'which links out to NCBI Pathogens Isolate Browser. ' +
kkonganti@11 20 " Default: ${params.gsrpy_url}",
kkonganti@11 21 cliflag: '-url',
kkonganti@11 22 clivalue: (params.gsrpy_url ? ' ' : '')
kkonganti@11 23 ]
kkonganti@11 24 ]
kkonganti@11 25
kkonganti@11 26 toolspecs.each {
kkonganti@11 27 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11 28 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11 29 }
kkonganti@11 30
kkonganti@11 31 return tool
kkonganti@11 32 }