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1 // Help text for sourmash sigkmers within CPIPES.
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2
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3 def sourmashsigkmersHelp(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 'sourmashsigkmers_run': [
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12 clihelp: 'Run `sourmash sigkmers` tool. Default: ' +
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13 (params.sourmashsigkmers_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 'sourmashsigkmers_k': [
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18 clihelp: 'The k-mer size to select. ' +
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19 "Default: ${params.sourmashsigkmers_k}",
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20 cliflag: '-k',
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21 clivalue: (params.sourmashsigkmers_k ?: '')
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22 ],
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23 'sourmashsigkmers_protein': [
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24 clihelp: 'Choose a protein signature. ' +
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25 "Default: ${params.sourmashsigkmers_protein}",
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26 cliflag: '--protein',
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27 clivalue: (params.sourmashsigkmers_protein ? ' ' : '')
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28 ],
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29 'sourmashsigkmers_noprotein': [
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30 clihelp: 'Do not choose a protein signature. ' +
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31 "Default: ${params.sourmashsigkmers_noprotein}",
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32 cliflag: '--no-protein',
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33 clivalue: (params.sourmashsigkmers_noprotein ? ' ' : '')
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34 ],
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35 'sourmashsigkmers_dayhoff': [
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36 clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
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37 "Default: ${params.sourmashsigkmers_dayhoff}",
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38 cliflag: '--dayhoff',
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39 clivalue: (params.sourmashsigkmers_dayhoff ? ' ' : '')
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40 ],
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41 'sourmashsigkmers_nodayhoff': [
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42 clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
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43 "Default: ${params.sourmashsigkmers_nodayhoff}",
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44 cliflag: '--no-dayhoff',
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45 clivalue: (params.sourmashsigkmers_nodayhoff ? ' ' : '')
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46 ],
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47 'sourmashsigkmers_hp': [
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48 clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
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49 "Default: ${params.sourmashsigkmers_hp}",
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50 cliflag: '--hp',
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51 clivalue: (params.sourmashsigkmers_hp ? ' ' : '')
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52 ],
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53 'sourmashsigkmers_nohp': [
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54 clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
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55 "Default: ${params.sourmashsigkmers_nohp}",
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56 cliflag: '--no-hp',
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57 clivalue: (params.sourmashsigkmers_nohp ? ' ' : '')
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58 ],
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59 'sourmashsigkmers_dna': [
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60 clihelp: 'Choose DNA signature. ' +
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61 "Default: ${params.sourmashsigkmers_dna}",
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62 cliflag: '--dna',
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63 clivalue: (params.sourmashsigkmers_dna ? ' ' : '')
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64 ],
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65 'sourmashsigkmers_nodna': [
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66 clihelp: 'Do not choose DNA signature. ' +
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67 "Default: ${params.sourmashsigkmers_nodna}",
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68 cliflag: '--no-dna',
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69 clivalue: (params.sourmashsigkmers_nodna ? ' ' : '')
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70 ],
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71 'sourmashsigkmers_save_kmers': [
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72 clihelp: 'Save k-mers and hash values to a CSV file. ' +
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73 "Default: ${params.sourmashsigkmers_save_kmers}",
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74 cliflag: null,
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75 clivalue: null
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76 ],
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77 'sourmashsigkmers_save_seqs': [
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78 clihelp: 'Save sequences with matching hash values to a FASTA file. ' +
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79 "Default: ${params.sourmashsigkmers_save_seqs}",
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80 cliflag: null,
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81 clivalue: null
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82 ],
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83 'sourmashsigkmers_translate': [
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84 clihelp: 'Translate DNA k-mers into amino acids (for protein, dayhoff, and hp sketches). ' +
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85 "Default: ${params.sourmashsigkmers_translate}",
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86 cliflag: '--translate',
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87 clivalue: (params.sourmashsigkmers_translate ? ' ' : '')
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88 ]
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89 ]
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90
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91 toolspecs.each {
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92 k, v -> tool.text['--' + k] = "${v.clihelp}"
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93 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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94 }
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95
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96 return tool
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97 } |
