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1 // Help text for kraken2 within CPIPES.
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2
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3 def kraken2Help(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 'kraken2_db': [
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12 clihelp: "Absolute path to kraken database. Default: ${params.kraken2_db}",
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13 cliflag: '--db',
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14 clivalue: null
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15 ],
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16 'kraken2_confidence': [
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17 clihelp: 'Confidence score threshold which must be ' +
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18 "between 0 and 1. Default: ${params.kraken2_confidence}",
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19 cliflag: '--confidence',
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20 clivalue: (params.kraken2_confidence ?: '')
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21 ],
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22 'kraken2_quick': [
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23 clihelp: "Quick operation (use first hit or hits). Default: ${params.kraken2_quick}",
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24 cliflag: '--quick',
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25 clivalue: (params.kraken2_quick ? ' ' : '')
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26 ],
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27 'kraken2_use_mpa_style': [
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28 clihelp: "Report output like Kraken 1's " +
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29 "kraken-mpa-report. Default: ${params.kraken2_use_mpa_style}",
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30 cliflag: '--use-mpa-style',
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31 clivalue: (params.kraken2_use_mpa_style ? ' ' : '')
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32 ],
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33 'kraken2_minimum_base_quality': [
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34 clihelp: 'Minimum base quality used in classification ' +
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35 " which is only effective with FASTQ input. Default: ${params.kraken2_minimum_base_quality}",
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36 cliflag: '--minimum-base-quality',
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37 clivalue: (params.kraken2_minimum_base_quality ?: '')
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38 ],
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39 'kraken2_report_zero_counts': [
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40 clihelp: 'Report counts for ALL taxa, even if counts are zero. ' +
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41 "Default: ${params.kraken2_report_zero_counts}",
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42 cliflag: '--report-zero-counts',
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43 clivalue: (params.kraken2_report_zero_counts ? ' ' : '')
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44 ],
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45 'kraken2_report_minmizer_data': [
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46 clihelp: 'Report minimizer and distinct minimizer count' +
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47 ' information in addition to normal Kraken report. ' +
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48 "Default: ${params.kraken2_report_minimizer_data}",
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49 cliflag: '--report-minimizer-data',
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50 clivalue: (params.kraken2_report_minimizer_data ? ' ' : '')
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51 ],
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52 'kraken2_use_names': [
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53 clihelp: 'Print scientific names instead of just taxids. ' +
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54 "Default: ${params.kraken2_use_names}",
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55 cliflag: '--use-names',
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56 clivalue: (params.kraken2_use_names ? ' ' : '')
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57 ],
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58 'kraken2_extract_bug': [
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59 clihelp: 'Extract the reads or contigs beloging to this bug. ' +
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60 "Default: ${params.kraken2_extract_bug}",
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61 cliflag: null,
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62 clivalue: null
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63 ]
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64 ]
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65
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66 toolspecs.each {
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67 k, v -> tool.text['--' + k] = "${v.clihelp}"
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68 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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69 }
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70
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71 return tool
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72 } |
