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1 // Help text for mash screen within CPIPES.
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2
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3 def mashscreenHelp(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 'mashscreen_run': [
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12 clihelp: 'Run `mash screen` tool. Default: ' +
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13 (params.mashscreen_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 'mashscreen_w': [
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18 clihelp: 'Winner-takes-all strategy for identity estimates. After counting ' +
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19 'hashes for each query, hashes that appear in multiple queries will ' +
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20 'be removed from all except the one with the best identity (ties ' +
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21 'broken by larger query), and other identities will be reduced. This ' +
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22 'removes output redundancy, providing a rough compositional outline. ' +
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23 " Default: ${params.mashscreen_w}",
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24 cliflag: '-w',
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25 clivalue: (params.mashscreen_w ? ' ' : '')
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26 ],
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27 'mashscreen_i': [
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28 clihelp: 'Minimum identity to report. Inclusive unless set to zero, in which ' +
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29 'case only identities greater than zero (i.e. with at least one ' +
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30 'shared hash) will be reported. Set to -1 to output everything. ' +
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31 "(-1-1). Default: ${params.mashscreen_i}",
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32 cliflag: '-i',
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33 clivalue: (params.mashscreen_i ?: '')
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34 ],
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35 'mashscreen_v': [
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36 clihelp: 'Maximum p-value to report (0-1). ' +
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37 "Default: ${params.mashscreen_v}",
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38 cliflag: '-v',
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39 clivalue: (params.mashscreen_v ?: '')
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40 ]
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41 ]
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42
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43 toolspecs.each {
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44 k, v -> tool.text['--' + k] = "${v.clihelp}"
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45 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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46 }
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47
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48 return tool
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49 } |
