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1 // Help text for `polypolish within CPIPES.
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2
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3 def polypolishHelp(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 'polypolish_run': [
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12 clihelp: 'Run polypolish tool. Default: ' +
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13 (params.polypolish_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 'polypolish_d': [
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18 clihelp: 'A base must occur at least this many times in the pileup to be considered valid. ' +
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19 "Default: ${params.polypolish_d}",
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20 cliflag: '-d',
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21 clivalue: (params.polypolish_d ?: '')
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22 ],
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23 'polypolish_i': [
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24 clihelp: 'A base must make up less than this fraction of the read depth to be considered invalid. ' +
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25 "Default: ${params.polypolish_i}",
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26 cliflag: '-i',
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27 clivalue: (params.polypolish_i ?: '')
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28 ],
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29 'polypolish_m': [
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30 clihelp: 'Ignore alignments with more than this many mismatches and indels. ' +
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31 "Default: ${params.polypolish_m}",
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32 cliflag: '-m',
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33 clivalue: (params.polypolish_m ?: '')
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34 ],
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35 'polypolish_v': [
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36 clihelp: 'A base must make up at least this fraction of the read depth to be considered valid. ' +
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37 "Default: ${params.polypolish_v}",
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38 cliflag: '-v',
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39 clivalue: (params.polypolish_v ?: '')
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40 ]
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41 ]
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42
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43 toolspecs.each {
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44 k, v -> tool.text['--' + k] = "${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 } |
