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1 // Help text for sourmash gather within CPIPES.
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2
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3 def sourmashgatherHelp(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 'sourmashgather_run': [
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12 clihelp: 'Run `sourmash gather` tool. Default: ' +
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13 (params.sourmashgather_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 'sourmashgather_n': [
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18 clihelp: 'Number of results to report. ' +
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19 'By default, will terminate at --sourmashgather_thr_bp value. ' +
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20 "Default: ${params.sourmashgather_n}",
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21 cliflag: '-n',
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22 clivalue: (params.sourmashgather_n ?: '')
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23 ],
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24 'sourmashgather_thr_bp': [
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25 clihelp: 'Reporting threshold (in bp) for estimated overlap with remaining query. ' +
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26 "Default: ${params.sourmashgather_thr_bp}",
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27 cliflag: '--threshold-bp',
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28 clivalue: (params.sourmashgather_thr_bp ?: '')
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29 ],
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30 'sourmashgather_ignoreabn': [
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31 clihelp: 'Do NOT use k-mer abundances if present. ' +
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32 "Default: ${params.sourmashgather_ignoreabn}",
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33 cliflag: '--ignore-abundance',
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34 clivalue: (params.sourmashgather_ignoreabn ? ' ' : '')
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35 ],
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36 'sourmashgather_prefetch': [
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37 clihelp: 'Use prefetch before gather. ' +
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38 "Default: ${params.sourmashgather_prefetch}",
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39 cliflag: '--prefetch',
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40 clivalue: (params.sourmashgather_prefetch ? ' ' : '')
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41 ],
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42 'sourmashgather_noprefetch': [
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43 clihelp: 'Do not use prefetch before gather. ' +
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44 "Default: ${params.sourmashgather_noprefetch}",
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45 cliflag: '--no-prefetch',
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46 clivalue: (params.sourmashgather_noprefetch ? ' ' : '')
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47 ],
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48 'sourmashgather_ani_ci': [
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49 clihelp: 'Output confidence intervals for ANI estimates. ' +
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50 "Default: ${params.sourmashgather_ani_ci}",
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51 cliflag: '--estimate-ani-ci',
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52 clivalue: (params.sourmashgather_ani_ci ? ' ' : '')
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53 ],
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54 'sourmashgather_k': [
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55 clihelp: 'The k-mer size to select. ' +
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56 "Default: ${params.sourmashgather_k}",
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57 cliflag: '-k',
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58 clivalue: (params.sourmashgather_k ?: '')
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59 ],
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60 'sourmashgather_protein': [
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61 clihelp: 'Choose a protein signature. ' +
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62 "Default: ${params.sourmashgather_protein}",
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63 cliflag: '--protein',
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64 clivalue: (params.sourmashgather_protein ? ' ' : '')
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65 ],
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66 'sourmashgather_noprotein': [
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67 clihelp: 'Do not choose a protein signature. ' +
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68 "Default: ${params.sourmashgather_noprotein}",
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69 cliflag: '--no-protein',
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70 clivalue: (params.sourmashgather_noprotein ? ' ' : '')
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71 ],
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72 'sourmashgather_dayhoff': [
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73 clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
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74 "Default: ${params.sourmashgather_dayhoff}",
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75 cliflag: '--dayhoff',
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76 clivalue: (params.sourmashgather_dayhoff ? ' ' : '')
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77 ],
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78 'sourmashgather_nodayhoff': [
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79 clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
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80 "Default: ${params.sourmashgather_nodayhoff}",
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81 cliflag: '--no-dayhoff',
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82 clivalue: (params.sourmashgather_nodayhoff ? ' ' : '')
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83 ],
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84 'sourmashgather_hp': [
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85 clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
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86 "Default: ${params.sourmashgather_hp}",
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87 cliflag: '--hp',
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88 clivalue: (params.sourmashgather_hp ? ' ' : '')
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89 ],
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90 'sourmashgather_nohp': [
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91 clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
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92 "Default: ${params.sourmashgather_nohp}",
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93 cliflag: '--no-hp',
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94 clivalue: (params.sourmashgather_nohp ? ' ' : '')
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95 ],
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96 'sourmashgather_dna': [
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97 clihelp: 'Choose DNA signature. ' +
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98 "Default: ${params.sourmashgather_dna}",
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99 cliflag: '--dna',
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100 clivalue: (params.sourmashgather_dna ? ' ' : '')
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101 ],
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102 'sourmashgather_nodna': [
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103 clihelp: 'Do not choose DNA signature. ' +
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104 "Default: ${params.sourmashgather_nodna}",
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105 cliflag: '--no-dna',
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106 clivalue: (params.sourmashgather_nodna ? ' ' : '')
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107 ],
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108 'sourmashgather_scaled': [
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109 clihelp: 'Scaled value should be between 100 and 1e6. ' +
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110 "Default: ${params.sourmashgather_scaled}",
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111 cliflag: '--scaled',
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112 clivalue: (params.sourmashgather_scaled ?: '')
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113 ],
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114 'sourmashgather_inc_pat': [
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115 clihelp: 'Search only signatures that match this pattern in name, filename, or md5. ' +
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116 "Default: ${params.sourmashgather_inc_pat}",
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117 cliflag: '--include-db-pattern',
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118 clivalue: (params.sourmashgather_inc_pat ?: '')
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119 ],
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120 'sourmashgather_exc_pat': [
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121 clihelp: 'Search only signatures that do not match this pattern in name, filename, or md5. ' +
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122 "Default: ${params.sourmashgather_exc_pat}",
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123 cliflag: '--exclude-db-pattern',
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124 clivalue: (params.sourmashgather_exc_pat ?: '')
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125 ]
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126 ]
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127
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128 toolspecs.each {
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129 k, v -> tool.text['--' + k] = "${v.clihelp}"
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130 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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131 }
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132
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133 return tool
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134 } |
