Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.0/lib/help/mlst.nf @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 def mlstHelp(params) {
kkonganti@101 2
kkonganti@101 3 Map tool = [:]
kkonganti@101 4 Map toolspecs = [:]
kkonganti@101 5 tool.text = [:]
kkonganti@101 6 tool.helpparams = [:]
kkonganti@101 7
kkonganti@101 8 toolspecs = [
kkonganti@101 9 'mlst_run': [
kkonganti@101 10 clihelp: "Run MLST tool. Default: ${params.mlst_run}",
kkonganti@101 11 cliflag: null,
kkonganti@101 12 clivalue: null
kkonganti@101 13 ],
kkonganti@101 14 'mlst_minid': [
kkonganti@101 15 clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " +
kkonganti@101 16 "Default: ${params.mlst_minid}",
kkonganti@101 17 cliflag: '--minid',
kkonganti@101 18 clivalue: (params.mlst_minid ?: 95)
kkonganti@101 19 ],
kkonganti@101 20 'mlst_mincov': [
kkonganti@101 21 clihelp: 'DNA %cov to report partial allele at all [?].' +
kkonganti@101 22 "Default: ${params.mlst_mincov}",
kkonganti@101 23 cliflag: '--mincov',
kkonganti@101 24 clivalue: (params.mlst_mincov ?: 10)
kkonganti@101 25 ],
kkonganti@101 26 'mlst_minscore': [
kkonganti@101 27 clihelp: 'Minumum score out of 100 to match a scheme.' +
kkonganti@101 28 "Default: ${params.mlst_minscore}",
kkonganti@101 29 cliflag: '--minscore',
kkonganti@101 30 clivalue: (params.mlst_minscore ?: 50)
kkonganti@101 31 ]
kkonganti@101 32 ]
kkonganti@101 33
kkonganti@101 34 toolspecs.each {
kkonganti@101 35 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@101 36 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@101 37 }
kkonganti@101 38
kkonganti@101 39 return tool
kkonganti@101 40 }