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annotate 0.7.0/lib/help/gsrpy.nf @ 21:4ce0e079377d tip

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 12:01:00 -0400
parents 0e7a0053e4a6
children
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kkonganti@17 1 // Help text for gen_salmon_res_table.py (gsrpy) within CPIPES.
kkonganti@17 2
kkonganti@17 3 def gsrpyHelp(params) {
kkonganti@17 4
kkonganti@17 5 Map tool = [:]
kkonganti@17 6 Map toolspecs = [:]
kkonganti@17 7 tool.text = [:]
kkonganti@17 8 tool.helpparams = [:]
kkonganti@17 9
kkonganti@17 10 toolspecs = [
kkonganti@17 11 'gsrpy_run': [
kkonganti@17 12 clihelp: 'Run the gen_salmon_res_table.py script. Default: ' +
kkonganti@17 13 (params.gsrpy_run ?: false),
kkonganti@17 14 cliflag: null,
kkonganti@17 15 clivalue: null
kkonganti@17 16 ],
kkonganti@17 17 'gsrpy_url': [
kkonganti@17 18 clihelp: 'Generate an additional column in final results table ' +
kkonganti@17 19 'which links out to NCBI Pathogens Isolate Browser. ' +
kkonganti@17 20 " Default: ${params.gsrpy_url}",
kkonganti@17 21 cliflag: '-url',
kkonganti@17 22 clivalue: (params.gsrpy_url ? ' ' : '')
kkonganti@17 23 ]
kkonganti@17 24 ]
kkonganti@17 25
kkonganti@17 26 toolspecs.each {
kkonganti@17 27 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17 28 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17 29 }
kkonganti@17 30
kkonganti@17 31 return tool
kkonganti@17 32 }