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1 // Help text for abricate within CPIPES.
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2
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3 def abricateHelp(params) {
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4
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5 Map tool = [:]
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6 Map toolspecs = [:]
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7 tool.text = [:]
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8 tool.helpparams = [:]
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9
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10 toolspecs = [
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11 'abricate_run': [
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12 clihelp: 'Run ABRicate tool. Default: ' +
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13 (params.abricate_run ?: false),
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14 cliflag: null,
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15 clivalue: null
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16 ],
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17 'abricate_minid': [
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18 clihelp: 'Minimum DNA %identity. ' +
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19 "Default: " + (params.abricate_minid ?: 80),
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20 cliflag: '--minid',
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21 clivalue: (params.abricate_minid ?: 80)
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22 ],
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23 'abricate_mincov': [
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24 clihelp: 'Minimum DNA %coverage. ' +
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25 "Default: " + (params.abricate_mincov ?: 80),
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26 cliflag: '--mincov',
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27 clivalue: (params.abricate_mincov ?: 80)
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28 ],
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29 'abricate_datadir': [
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30 clihelp: 'ABRicate databases folder. ' +
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31 "Default: " + (params.abricate_datadir ?: 'undefined'),
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32 cliflag: '--datadir',
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33 clivalue: (params.abricate_datadir ?: '')
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34 ]
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35 ]
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36
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37 toolspecs.each {
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38 k, v -> tool.text['--' + k] = "${v.clihelp}"
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39 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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40 }
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41
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42 return tool
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43 } |
