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1 // Help text for shovill within CPIPES.
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2
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3 def shovillHelp(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 'shovill_run': [
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12 clihelp: 'Run shovill tool. Default: ' +
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13 (params.shovill_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 'shovill_depth': [
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18 clihelp: 'Sub-sample R1/R2 to this depth. Disable with --shovill_depth 0. ' +
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19 "Default: ${params.shovill_depth}",
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20 cliflag: '--depth',
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21 clivalue: (params.shovill_depth ?: 150)
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22 ],
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23 'shovill_gsize': [
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24 clihelp: 'Estimated genome size eg. 3.2M. <false=AUTODETECT>. ' +
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25 "Default: ${params.shovill_gsize}",
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26 cliflag: '--gsize',
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27 clivalue: (params.shovill_gsize ?: '')
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28 ],
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29 'shovill_minlen': [
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30 clihelp: 'Minimum contig length. <false=AUTO>. ' +
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31 "Default: ${params.shovill_minlen}",
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32 cliflag: '--minlen',
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33 clivalue: (params.shovill_minlen ?: '')
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34 ],
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35 'shovill_mincov': [
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36 clihelp: "Minimum contig coverage. <false=AUTO>. " +
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37 "Default: ${params.shovill_mincov}",
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38 cliflag: '--mincov',
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39 clivalue: (params.shovill_mincov ?: '')
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40 ],
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41 'shovill_namefmt': [
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42 clihelp: "Format of contig FASTA IDs in 'printf' style. " +
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43 "Default: ${params.shovill_namefmt}",
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44 cliflag: '--namefmt',
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45 clivalue: (params.shovill_namefmt ?: '')
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46 ],
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47 'shovill_keepfiles': [
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48 clihelp: 'Keep intermediate files. ' +
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49 "Default: ${params.shovill_keepfiles}",
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50 cliflag: '--keepfiles',
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51 clivalue: (params.shovill_keepfiles ? ' ' : '')
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52 ],
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53 'shovill_assembler': [
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54 clihelp: 'Assembler: skesa, megahit, velvet, or spades. ' +
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55 "Default: ${params.shovill_assembler}",
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56 cliflag: '--assembler',
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57 clivalue: (params.shovill_assembler ?: '')
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58 ],
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59 'shovill_opts': [
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60 clihelp: "Extra assembler options in quotes. Ex: '--sc'. " +
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61 "Default: ${params.shovill_opts}",
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62 cliflag: '--opts',
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63 clivalue: (params.shovill_opts ?: '')
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64 ],
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65 'shovill_kmers': [
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66 clihelp: 'K-mers to use. <false=AUTO>. ' +
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67 "Default: ${params.shovill_kmers}",
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68 cliflag: '--kmers',
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69 clivalue: (params.shovill_kmers ?: '')
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70 ],
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71 'shovill_trim': [
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72 clihelp: 'Enable adator trimming. ' +
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73 "Default: ${params.shovill_trim}",
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74 cliflag: '--trim',
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75 clivalue: (params.shovill_trim ? ' ' : '')
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76 ],
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77 'shovill_noreadcorr': [
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78 clihelp: 'Disable read error correction. ' +
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79 "Default: ${params.shovill_noreadcorr}",
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80 cliflag: '--noreadcorr',
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81 clivalue: (params.shovill_noreadcorr ? ' ' : '')
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82 ],
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83 'shovill_nostitch': [
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84 clihelp: 'Disable read stitching. ' +
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85 "Default: ${params.shovill_nostitch}",
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86 cliflag: '--nostitch',
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87 clivalue: (params.shovill_nostitch ? ' ' : '')
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88 ],
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89 'shovill_nocorr': [
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90 clihelp: 'Disable post-assembly correction. ' +
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91 "Default: ${params.shovill_nocorr}",
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92 cliflag: '--nocorr',
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93 clivalue: (params.shovill_nocorr ? ' ' : '')
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94 ]
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95 ]
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96
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97 toolspecs.each {
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98 k, v -> tool.text['--' + k] = "${v.clihelp}"
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99 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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100 }
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101
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102 return tool
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103 } |
