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1 // Help text for NanoPlot within CPIPES.
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2
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3 def nanoplotHelp(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 'nanoplot_run': [
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12 clihelp: 'Run NanoPlot tool on ONT reads. Default: ' +
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13 (params.nanoplot_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 'nanoplot_store': [
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18 clihelp: 'Store the extracted data in a pickle file for future plotting. ' +
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19 "Default: ${params.nanoplot_store}",
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20 cliflag: '--store',
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21 clivalue: (params.nanoplot_store ? ' ' : '')
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22 ],
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23 'nanoplot_raw': [
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24 clihelp: 'Store the extracted data in tab separated file. ' +
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25 "Default: ${params.nanoplot_raw}",
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26 cliflag: '--raw',
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27 clivalue: (params.nanoplot_raw ? ' ' : '')
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28 ],
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29 'nanoplot_huge': [
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30 clihelp: 'Input data is one very large file. ' +
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31 "Default: ${params.nanoplot_huge}",
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32 cliflag: '--huge',
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33 clivalue: (params.nanoplot_huge ? ' ' : '')
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34 ],
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35 'nanoplot_no_static': [
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36 clihelp: 'Do not make static (png) plots. ' +
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37 "Default: ${params.nanoplot_no_static}",
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38 cliflag: '--no_static',
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39 clivalue: (params.nanoplot_no_static ? ' ' : '')
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40 ],
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41 'nanoplot_tsv_stats': [
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42 clihelp: 'Output the stats file as a properly formatted TSV. ' +
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43 "Default: ${params.nanoplot_tsv_stats}",
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44 cliflag: '--tsv_stats',
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45 clivalue: (params.nanoplot_tsv_stats ? ' ' : '')
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46 ],
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47 'nanoplot_only_report': [
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48 clihelp: 'Output only the report. ' +
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49 "Default: ${params.nanoplot_only_report}",
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50 cliflag: '--only-report',
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51 clivalue: (params.nanoplot_only_report ? ' ' : '')
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52 ],
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53 'nanoplot_minlength': [
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54 clihelp: "Hide reads shorter than length specified. " +
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55 "Default: ${params.nanoplot_minlength}",
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56 cliflag: '--minlength',
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57 clivalue: (params.nanoplot_minlength ?: '')
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58 ],
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59 'nanoplot_maxlength': [
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60 clihelp: 'Hide reads longer than length specified. ' +
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61 "Default: ${params.nanoplot_maxlength}",
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62 cliflag: '--maxlength',
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63 clivalue: (params.nanoplot_maxlength ?: '')
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64 ],
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65 'nanoplot_downsample': [
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66 clihelp: 'Reduce dataset to N reads by random sampling. ' +
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67 "Default: ${params.nanoplot_downsample}",
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68 cliflag: '--downsample',
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69 clivalue: (params.nanoplot_downsample ?: '')
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70 ],
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71 'nanoplot_drop_outliers': [
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72 clihelp: 'Drop outlier reads with extreme long length. ' +
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73 "Default: ${params.nanoplot_drop_outliers}",
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74 cliflag: '--drop_outliers',
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75 clivalue: (params.nanoplot_drop_outliers ? ' ' : '')
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76 ],
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77 'nanoplot_loglength': [
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78 clihelp: 'Additionally show logarithmic scaling of lengths in plots. ' +
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79 "Default: ${params.nanoplot_loglength}",
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80 cliflag: '--loglength',
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81 clivalue: (params.nanoplot_loglength ?: '')
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82 ],
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83 'nanoplot_perc_qual': [
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84 clihelp: 'Weight given to the window quality score. ' +
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85 "Default: ${params.nanoplot_perc_qual}",
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86 cliflag: '--percentqual',
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87 clivalue: (params.nanoplot_perc_qual ? ' ' : '')
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88 ],
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89 'nanoplot_alength': [
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90 clihelp: 'Use aligned read lengths rather than sequenced length (bam mode). ' +
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91 "Default: ${params.nanoplot_alength}",
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92 cliflag: '--alength',
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93 clivalue: (params.nanoplot_alength ? ' ' : '')
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94 ],
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95 'nanoplot_minqual': [
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96 clihelp: 'Drop reads with an average quality lower than specified. ' +
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97 "Default: ${params.nanoplot_minqual}",
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98 cliflag: '--minqual',
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99 clivalue: (params.nanoplot_minqual ?: '')
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100 ],
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101 'nanoplot_runtime_until': [
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102 clihelp: 'Only tke the N first hours of a run. ' +
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103 "Default: ${params.nanoplot_runtime_until}",
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104 cliflag: '--runtime_until',
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105 clivalue: (params.nanoplot_runtime_until ?: '')
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106 ],
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107 'nanoplot_readtype': [
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108 clihelp: 'Which read type to extract information about from summary. ' +
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109 'Options are 1D, 2D, 1D2. ' +
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110 "Default: ${params.nanoplot_readtype}",
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111 cliflag: '--readtype',
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112 clivalue: (params.nanoplot_readtype ?: '')
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113 ],
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114 'nanoplot_barcoded': [
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115 clihelp: 'Split the summary file by barcode. ' +
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116 "Default: ${params.nanoplot_barcoded}",
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117 cliflag: '--barcoded',
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118 clivalue: (params.nanoplot_barcoded ? ' ' : '')
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119 ],
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120 'nanoplot_no_supp': [
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121 clihelp: 'Remove supplementary alignments. ' +
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122 "Default: ${params.nanoplot_no_supp}",
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123 cliflag: '--no_supplementary',
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124 clivalue: (params.nanoplot_no_supp ? ' ' : '')
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125 ],
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126 'nanoplot_c': [
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127 clihelp: 'Specify a valid matplotlib color for the plots. ' +
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128 "Default: ${params.nanoplot_c}",
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129 cliflag: '-c',
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130 clivalue: (params.nanoplot_c ?: '')
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131 ],
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132 'nanoplot_cm': [
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133 clihelp: 'Specify a valid matplotlib colormap for the heatmap. ' +
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134 "Default: ${params.nanoplot_cm}",
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135 cliflag: '-cm',
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136 clivalue: (params.nanoplot_cm ?: '')
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137 ],
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138 'nanoplot_format': [
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139 clihelp: 'Specify the output format of the plots, which are in addition to the html files. ' +
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140 "Default: ${params.nanoplot_format}",
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141 cliflag: '-f',
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142 clivalue: (params.nanoplot_format ?: '')
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143 ],
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144 'nanoplot_plots': [
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145 clihelp: 'Specify which bivariate plots have to be made [ kde, hex, dot ]. ' +
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146 "Default: ${params.nanoplot_plots}",
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147 cliflag: '--plots',
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148 clivalue: (params.nanoplot_plots ?: '')
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149 ],
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150 'nanoplot_noN50': [
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151 clihelp: 'Hide the N50 mark in the read length histogram. ' +
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152 "Default: ${params.nanoplot_noN50}",
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153 cliflag: '--no-N50',
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154 clivalue: (params.nanoplot_noN50 ?: '')
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155 ],
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156 'nanoplot_N50': [
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157 clihelp: 'Show the N50 mark in the read length histogram. ' +
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158 "Default: ${params.nanoplot_N50}",
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159 cliflag: '--N50',
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160 clivalue: (params.nanoplot_N50 ?: '')
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161 ],
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162 'nanoplot_dpi': [
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163 clihelp: 'Set the DPI for saving images. ' +
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164 "Default: ${params.nanoplot_dpi}",
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165 cliflag: '--dpi',
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166 clivalue: (params.nanoplot_dpi ?: '')
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167 ],
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168 'nanoplot_hide_stats': [
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169 clihelp: 'Do not add Pearson R stats in some bivariate plots. ' +
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170 "Default: ${params.nanoplot_hide_stats}",
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171 cliflag: '--hide_stats',
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172 clivalue: (params.nanoplot_hide_stats ?: '')
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173 ]
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174 ]
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175
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176 toolspecs.each {
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177 k, v -> tool.text['--' + k] = "${v.clihelp}"
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178 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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179 }
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180
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181 return tool
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182 } |
