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