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1 // Help text for kma align within CPIPES.
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2
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3 def kmaalignHelp(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 'kmaalign_run': [
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12 clihelp: 'Run kma tool. Default: ' +
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13 (params.kmaalign_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 'kmaalign_int': [
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18 clihelp: 'Input file has interleaved reads. ' +
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19 " Default: ${params.kmaalign_int}",
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20 cliflag: '-int',
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21 clivalue: (params.kmaalign_int ? ' ' : '')
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22 ],
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23 'kmaalign_ef': [
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24 clihelp: 'Output additional features. ' +
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25 "Default: ${params.kmaalign_ef}",
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26 cliflag: '-ef',
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27 clivalue: (params.kmaalign_ef ? ' ' : '')
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28 ],
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29 'kmaalign_vcf': [
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30 clihelp: 'Output vcf file. 2 to apply FT. ' +
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31 "Default: ${params.kmaalign_vcf}",
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32 cliflag: '-vcf',
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33 clivalue: (params.kmaalign_vcf ? ' ' : '')
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34 ],
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35 'kmaalign_sam': [
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36 clihelp: 'Output SAM, 4/2096 for mapped/aligned. ' +
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37 "Default: ${params.kmaalign_sam}",
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38 cliflag: '-sam',
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39 clivalue: (params.kmaalign_sam ? ' ' : '')
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40 ],
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41 'kmaalign_nc': [
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42 clihelp: 'No consensus file. ' +
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43 "Default: ${params.kmaalign_nc}",
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44 cliflag: '-nc',
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45 clivalue: (params.kmaalign_nc ? ' ' : '')
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46 ],
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47 'kmaalign_na': [
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48 clihelp: 'No aln file. ' +
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49 "Default: ${params.kmaalign_na}",
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50 cliflag: '-na',
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51 clivalue: (params.kmaalign_na ? ' ' : '')
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52 ],
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53 'kmaalign_nf': [
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54 clihelp: 'No frag file. ' +
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55 "Default: ${params.kmaalign_nf}",
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56 cliflag: '-nf',
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57 clivalue: (params.kmaalign_nf ? ' ' : '')
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58 ],
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59 'kmaalign_a': [
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60 clihelp: 'Output all template mappings. ' +
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61 "Default: ${params.kmaalign_a}",
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62 cliflag: '-a',
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63 clivalue: (params.kmaalign_a ? ' ' : '')
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64 ],
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65 'kmaalign_and': [
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66 clihelp: 'Use both -mrs and p-value on consensus. ' +
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67 "Default: ${params.kmaalign_and}",
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68 cliflag: '-and',
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69 clivalue: (params.kmaalign_and ? ' ' : '')
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70 ],
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71 'kmaalign_oa': [
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72 clihelp: 'Use neither -mrs or p-value on consensus. ' +
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73 "Default: ${params.kmaalign_oa}",
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74 cliflag: '-oa',
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75 clivalue: (params.kmaalign_oa ? ' ' : '')
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76 ],
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77 'kmaalign_bc': [
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78 clihelp: 'Minimum support to call bases. ' +
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79 "Default: ${params.kmaalign_bc}",
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80 cliflag: '-bc',
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81 clivalue: (params.kmaalign_bc ?: '')
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82 ],
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83 'kmaalign_bcNano': [
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84 clihelp: 'Altered indel calling for ONT data. ' +
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85 "Default: ${params.kmaalign_bcNano}",
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86 cliflag: '-bcNano',
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87 clivalue: (params.kmaalign_bcNano ? ' ' : '')
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88 ],
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89 'kmaalign_bcd': [
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90 clihelp: 'Minimum depth to call bases. ' +
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91 "Default: ${params.kmaalign_bcd}",
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92 cliflag: '-bcd',
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93 clivalue: (params.kmaalign_bcd ?: '')
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94 ],
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95 'kmaalign_bcg': [
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96 clihelp: 'Maintain insignificant gaps. ' +
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97 "Default: ${params.kmaalign_bcg}",
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98 cliflag: '-bcg',
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99 clivalue: (params.kmaalign_bcg ? ' ' : '')
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100 ],
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101 'kmaalign_ID': [
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102 clihelp: 'Minimum consensus ID. ' +
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103 "Default: ${params.kmaalign_ID}",
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104 cliflag: '-ID',
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105 clivalue: (params.kmaalign_ID ?: '')
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106 ],
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107 'kmaalign_md': [
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108 clihelp: 'Minimum depth. ' +
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109 "Default: ${params.kmaalign_md}",
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110 cliflag: '-md',
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111 clivalue: (params.kmaalign_md ?: '')
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112 ],
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113 'kmaalign_dense': [
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114 clihelp: 'Skip insertion in consensus. ' +
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115 "Default: ${params.kmaalign_dense}",
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116 cliflag: '-dense',
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117 clivalue: (params.kmaalign_dense ? ' ' : '')
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118 ],
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119 'kmaalign_ref_fsa': [
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120 clihelp: 'Use Ns on indels. ' +
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121 "Default: ${params.kmaalign_ref_fsa}",
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122 cliflag: '-ref_fsa',
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123 clivalue: (params.kmaalign_ref_fsa ? ' ' : '')
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124 ],
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125 'kmaalign_Mt1': [
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126 clihelp: 'Map everything to one template. ' +
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127 "Default: ${params.kmaalign_Mt1}",
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128 cliflag: '-Mt1',
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129 clivalue: (params.kmaalign_Mt1 ? ' ' : '')
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130 ],
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131 'kmaalign_1t1': [
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132 clihelp: 'Map one query to one template. ' +
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133 "Default: ${params.kmaalign_1t1}",
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134 cliflag: '-1t1',
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135 clivalue: (params.kmaalign_1t1 ? ' ' : '')
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136 ],
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137 'kmaalign_mrs': [
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138 clihelp: 'Minimum relative alignment score. ' +
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139 "Default: ${params.kmaalign_mrs}",
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140 cliflag: '-mrs',
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141 clivalue: (params.kmaalign_mrs ?: '')
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142 ],
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143 'kmaalign_mrc': [
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144 clihelp: 'Minimum query coverage. ' +
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145 "Default: ${params.kmaalign_mrc}",
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146 cliflag: '-mrc',
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147 clivalue: (params.kmaalign_mrc ?: '')
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148 ],
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149 'kmaalign_mp': [
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150 clihelp: 'Minimum phred score of trailing and leading bases. ' +
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151 "Default: ${params.kmaalign_mp}",
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152 cliflag: '-mp',
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153 clivalue: (params.kmaalign_mp ?: '')
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154 ],
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155 'kmaalign_mq': [
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156 clihelp: 'Set the minimum mapping quality. ' +
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157 "Default: ${params.kmaalign_mq}",
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158 cliflag: '-mq',
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159 clivalue: (params.kmaalign_mq ?: '')
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160 ],
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161 'kmaalign_eq': [
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162 clihelp: 'Minimum average quality score. ' +
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163 "Default: ${params.kmaalign_eq}",
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164 cliflag: '-eq',
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165 clivalue: (params.kmaalign_eq ?: '')
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166 ],
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167 'kmaalign_5p': [
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168 clihelp: 'Trim 5 prime by this many bases. ' +
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169 "Default: ${params.kmaalign_5p}",
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170 cliflag: '-5p',
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171 clivalue: (params.kmaalign_5p ?: '')
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172 ],
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173 'kmaalign_3p': [
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174 clihelp: 'Trim 3 prime by this many bases ' +
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175 "Default: ${params.kmaalign_3p}",
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176 cliflag: '-3p',
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177 clivalue: (params.kmaalign_3p ?: '')
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178 ],
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179 'kmaalign_apm': [
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180 clihelp: 'Sets both -pm and -fpm ' +
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181 "Default: ${params.kmaalign_apm}",
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182 cliflag: '-apm',
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183 clivalue: (params.kmaalign_apm ?: '')
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184 ],
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185 'kmaalign_cge': [
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186 clihelp: 'Set CGE penalties and rewards ' +
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187 "Default: ${params.kmaalign_cge}",
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188 cliflag: '-cge',
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189 clivalue: (params.kmaalign_cge ? ' ' : '')
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190 ],
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191
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192 ]
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193
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194 toolspecs.each {
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195 k, v -> tool.text['--' + k] = "${v.clihelp}"
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196 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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197 }
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198
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199 return tool
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200 } |
