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1 // Help text for prokka within CPIPES.
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2
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3 def prokkaHelp(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 'prokka_run': [
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12 clihelp: 'Run prokka tool. Default: ' +
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13 (params.prokka_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 'prokka_dbdir': [
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18 clihelp: 'Path to prokka database root folder. ' +
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19 "Default: ${params.prokka_dbdir}",
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20 cliflag: '--dbdir',
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21 clivalue: (params.prokka_dbdir ?: '')
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22 ],
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23 'prokka_addgenes': [
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24 clihelp: "Add 'gene' features for each 'CDS' feature. " +
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25 "Default: ${params.prokka_addgenes}",
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26 cliflag: '--addgenes',
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27 clivalue: (params.prokka_addgenes ? ' ' : '')
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28 ],
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29 'prokka_addmrna': [
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30 clihelp: "Add 'mRNA' features for each 'CDS' feature. " +
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31 "Default: ${params.prokka_addmrna}",
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32 cliflag: '--addmrna',
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33 clivalue: (params.prokka_addmrna ? ' ' : '')
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34 ],
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35 'prokka_locustag': [
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36 clihelp: "Locus tag prefix. " +
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37 "Default: ${params.prokka_locustag}",
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38 cliflag: '--locustag',
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39 clivalue: (params.prokka_locustag ?: '')
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40 ],
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41 'prokka_increment': [
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42 clihelp: "Locus tag counter increment. " +
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43 "Default: ${params.prokka_increment}",
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44 cliflag: '--increment',
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45 clivalue: (params.prokka_increment ?: '')
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46 ],
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47 'prokka_gffver': [
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48 clihelp: 'GFF version. ' +
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49 "Default: ${params.prokka_gffver}",
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50 cliflag: '-gffver',
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51 clivalue: (params.prokka_gffver ?: '')
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52 ],
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53 'prokka_compliant': [
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54 clihelp: ' Force Genbank/ENA/DDJB compliance i.e. ' +
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55 '--prokka_addgenes --prokka_mincontiglen 200 --prokka_centre XXX. ' +
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56 "Default: ${params.prokka_compliant}",
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57 cliflag: '--compliant',
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58 clivalue: (params.prokka_compliant ? ' ' : '')
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59 ],
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60 'prokka_centre': [
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61 clihelp: 'Sequencing centre ID. ' +
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62 "Default: ${params.prokka_centre}",
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63 cliflag: '--centre',
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64 clivalue: (params.prokka_centre ?: '')
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65 ],
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66 'prokka_accver': [
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67 clihelp: 'Version to put in GenBank file. ' +
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68 "Default: ${params.prokka_accver}",
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69 cliflag: '--accver',
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70 clivalue: (params.prokka_accver ?: '')
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71 ],
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72 'prokka_genus': [
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73 clihelp: 'Genus name. ' +
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74 "Default: ${params.prokka_genus}",
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75 cliflag: '--genus',
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76 clivalue: (params.prokka_genus ?: '')
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77 ],
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78 'prokka_species': [
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79 clihelp: 'Species name. ' +
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80 "Default: ${params.prokka_species}",
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81 cliflag: '--species',
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82 clivalue: (params.prokka_species ?: '')
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83 ],
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84 'prokka_strain': [
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85 clihelp: 'Strain name. ' +
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86 "Default: ${params.prokka_strain}",
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87 cliflag: '--strain',
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88 clivalue: (params.prokka_strain ?: '')
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89 ],
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90 'prokka_plasmid': [
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91 clihelp: 'Plasmid name or identifier. ' +
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92 "Default: ${params.prokka_plasmid}",
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93 cliflag: '--plasmid',
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94 clivalue: (params.prokka_plasmid ?: '')
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95 ],
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96 'prokka_kingdom': [
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97 clihelp: 'Annotation mode: Archaea|Bacteria|Mitochondria|Viruses. ' +
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98 "Default: ${params.prokka_kingdom}",
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99 cliflag: '--kingdom',
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100 clivalue: (params.prokka_kingdom ?: '')
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101 ],
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102 'prokka_gcode': [
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103 clihelp: 'Genetic code / Translation table (set if --prokka_kingdom is set). ' +
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104 "Default: ${params.prokka_gcode}",
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105 cliflag: '--gcode',
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106 clivalue: (params.prokka_gcode ?: '')
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107 ],
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108 'prokka_usegenus': [
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109 clihelp: 'Use genus-specific BLAST databases (needs --prokka_genus) ' +
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110 "Default: ${params.prokka_usegenus}",
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111 cliflag: '--usegenus',
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112 clivalue: (params.prokka_usegenus ? ' ' : '')
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113 ],
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114 'prokka_metagenome': [
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115 clihelp: 'Improve gene predictions for highly fragmented genomes. ' +
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116 "Default: ${params.prokka_metagenome}",
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117 cliflag: '--metagenome',
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118 clivalue: (params.prokka_metagenome ? ' ' : '')
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119 ],
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120 'prokka_rawproduct': [
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121 clihelp: 'Version to put in GenBank file. ' +
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122 "Default: ${params.prokka_rawproduct}",
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123 cliflag: '--rawproduct',
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124 clivalue: (params.prokka_rawproduct ?: '')
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125 ],
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126 'prokka_cdsrnaolap': [
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127 clihelp: 'Do not clean up /product annotation. ' +
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128 "Default: ${params.prokka_cdsrnaolap}",
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129 cliflag: '--cdsrnaolap',
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130 clivalue: (params.prokka_cdsrnaolap ? ' ' : '')
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131 ],
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132 'prokka_evalue': [
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133 clihelp: 'Similarity e-value cut-off. ' +
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134 "Default: ${params.prokka_evalue}",
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135 cliflag: '--evalue',
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136 clivalue: (params.prokka_evalue ?: '')
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137 ],
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138 'prokka_coverage': [
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139 clihelp: 'Minimum coverage on query protein. ' +
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140 "Default: ${params.prokka_coverage}",
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141 cliflag: '--coverage',
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142 clivalue: (params.prokka_coverage ?: '')
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143 ],
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144 'prokka_fast': [
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145 clihelp: 'Fast mode - only use basic BLASTP databases. ' +
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146 "Default: ${params.prokka_fast}",
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147 cliflag: '--fast',
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148 clivalue: (params.prokka_fast ? ' ' : '')
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149 ],
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150 'prokka_noanno': [
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151 clihelp: 'For CDS just set /product="unannotated protein". ' +
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152 "Default: ${params.prokka_noanno}",
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153 cliflag: '--noanno',
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154 clivalue: (params.prokka_noanno ? ' ' : '')
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155 ],
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156 'prokka_mincontiglen': [
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157 clihelp: 'Minimum contig size [NCBI needs 200]. ' +
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158 "Default: ${params.prokka_mincontiglen}",
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159 cliflag: '--mincontiglen',
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160 clivalue: (params.prokka_mincontiglen ?: '')
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161 ],
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162 'prokka_rfam': [
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163 clihelp: 'Enable searching for ncRNAs with Infernal+Rfam (SLOW!). ' +
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164 "Default: ${params.prokka_rfam}",
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165 cliflag: '--rfam',
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166 clivalue: (params.prokka_rfam ? ' ' : '')
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167 ],
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168 'prokka_norrna': [
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169 clihelp: "Don't run rRNA search. " +
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170 "Default: ${params.prokka_norrna}",
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171 cliflag: '--norrna',
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172 clivalue: (params.prokka_norrna ? ' ' : '')
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173 ],
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174 'prokka_notrna': [
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175 clihelp: "Don't run tRNA search. " +
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176 "Default: ${params.prokka_notrna}",
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177 cliflag: '--notrna',
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178 clivalue: (params.prokka_notrna ? ' ' : '')
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179 ],
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180 'prokka_rnammer': [
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181 clihelp: 'Prefer RNAmmer over Barrnap for rRNA prediction. ' +
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182 "Default: ${params.prokka_rnammer}",
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183 cliflag: '--rnammer',
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184 clivalue: (params.prokka_rnammer ? ' ' : '')
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185 ]
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186 ]
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187
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188 toolspecs.each {
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189 k, v -> tool.text['--' + k] = "${v.clihelp}"
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190 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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191 }
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192
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193 return tool
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194 } |
