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1 // Help text for quast within CPIPES.
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2
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3 def quastHelp(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 'quast_run': [
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12 clihelp: 'Run quast tool. Default: ' +
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13 (params.quast_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 'quast_min_contig': [
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18 clihelp: 'Lower threshold for contig length. ' +
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19 "Default: ${params.quast_min_contig}",
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20 cliflag: '-m',
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21 clivalue: (params.quast_min_contig ?: '')
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22 ],
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23 'quast_split_scaffolds': [
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24 clihelp: "Split assemblies by continuous fragments of N's" +
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25 'and add such "contigs" to the comparison' +
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26 "Default: ${params.quast_split_scaffolds}",
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27 cliflag: '-s',
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28 clivalue: (params.quast_split_scaffolds ? ' ' : '')
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29 ],
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30 'quast_euk': [
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31 clihelp: 'Genome is eukaryotic (primarily affects gene prediction). ' +
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32 "Default: ${params.quast_euk}",
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33 cliflag: '-e',
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34 clivalue: (params.quast_euk ? ' ' : '')
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35 ],
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36 'quast_fungal': [
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37 clihelp: 'Genome is fungal (primarily affects gene prediction). ' +
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38 "Default: ${params.quast_fungal}",
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39 cliflag: '--fungal',
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40 clivalue: (params.quast_fungal ? ' ' : '')
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41 ],
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42 'quast_large': [
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43 clihelp: 'Use optimal parameters for evaluation of large genomes' +
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44 "In particular, imposes '-e -m 3000 -i 500 -x 7000'." +
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45 "Default: ${params.quast_large}",
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46 cliflag: '--large',
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47 clivalue: (params.quast_large ? ' ' : '')
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48 ],
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49 'quast_k': [
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50 clihelp: 'Compute k-mer-based quality metrics (recommended for large genomes). ' +
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51 "Default: ${params.quast_k}",
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52 cliflag: '-k',
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53 clivalue: (params.quast_k ? ' ' : '')
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54 ],
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55 'quast_kmer_size': [
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56 clihelp: 'Size of k used in --quast_k. ' +
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57 "Default: ${params.quast_kmer_size}",
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58 cliflag: '--k-mer-size',
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59 clivalue: (params.quast_kmer_size ?: 101)
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60 ],
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61 'quast_circos': [
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62 clihelp: 'Draw circos plot. ' +
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63 "Default: ${params.quast_circos}",
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64 cliflag: '--circos',
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65 clivalue: (params.quast_circos ? ' ' : '')
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66 ],
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67 'quast_glimmer': [
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68 clihelp: 'Use GlimmerHMM for gene prediction. ' +
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69 "Default: ${params.quast_glimmer}",
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70 cliflag: '--glimmer',
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71 clivalue: (params.quast_glimmer ? ' ' : '')
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72 ],
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73 'quast_gene_thr': [
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74 clihelp: 'Comma-separated list of threshold lengths of genes to ' +
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75 'search with Gene Finding module. ' +
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76 "Default: ${params.quast_gene_thr}",
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77 cliflag: '--gene-thresholds',
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78 clivalue: (params.quast_gene_thr ?: '')
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79 ],
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80 'quast_rna_finding': [
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81 clihelp: 'Predict ribosomal RNA genes using Barrnap. ' +
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82 "Default: ${params.quast_rna_finding}",
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83 cliflag: '--rna-finding',
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84 clivalue: (params.quast_rna_finding ? ' ' : '')
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85 ],
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86 'quast_ref_size': [
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87 clihelp: 'Estimated reference size in-case the reference genome is not supplied. ' +
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88 "Default: ${params.quast_ref_size}",
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89 cliflag: '--est-ref-size',
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90 clivalue: (params.quast_ref_size ?: '')
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91 ],
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92 'quast_ctg_thr': [
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93 clihelp: 'Comma-separated list of contig length thresholds. ' +
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94 "Default: ${params.quast_ctg_thr}",
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95 cliflag: '--contig-thresholds',
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96 clivalue: (params.quast_ctg_thr ?: '')
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97 ],
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98 'quast_x_for_nx': [
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99 clihelp: "Value of 'x' for Nx, Lx, etc metrics reported in addition to N50, L50, etc. " +
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100 "Default: ${params.quast_x_for_nx}",
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101 cliflag: '--x-for-Nx',
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102 clivalue: (params.quast_x_for_nx ?: '')
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103 ],
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104 'quast_use_all_alns': [
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105 clihelp: 'Compute genome fraction, # genes, # operons in QUAST v1.* style. ' +
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106 "By default, QUAST filters Minimap's alignments to keep only best ones. " +
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107 "Default: ${params.quast_glimmer}",
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108 cliflag: '--use-all-alignments',
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109 clivalue: (params.quast_use_all_alns ? ' ' : '')
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110 ],
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111 'quast_min_alignment': [
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112 clihelp: 'The minimum alignment length. ' +
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113 "Default: ${params.quast_min_alignment}",
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114 cliflag: '-i',
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115 clivalue: (params.quast_min_alignment ?: '')
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116 ],
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117 'quast_min_identity': [
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118 clihelp: 'The minimum alignment identity (80.0, 100.0). ' +
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119 "Default: ${params.quast_min_identity}",
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120 cliflag: '--min-identity',
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121 clivalue: (params.quast_min_identity ?: '')
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122 ],
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123 'quast_ambig_usage': [
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124 clihelp: 'Use none, one, or all alignments of a contig when all of them. ' +
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125 'are almost equally good (see --quast_ambig_score). ' +
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126 "Default: ${params.quast_ambig_usage}",
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127 cliflag: '-a',
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128 clivalue: (params.quast_ambig_usage ?: '')
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129 ],
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130 'quast_ambig_score': [
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131 clihelp: 'Score S for defining equally good alignments of a single contig. ' +
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132 'All alignments are sorted by decreasing LEN * IDY% value. ' +
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133 'All alignments with LEN * IDY% < S * best(LEN * IDY%) are ' +
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134 'discarded. S should be between 0.8 and 1.0. ' +
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135 "Default: ${params.quast_ambig_score}",
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136 cliflag: '--ambiguity-score',
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137 clivalue: (params.quast_ambig_score ?: '')
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138 ],
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139 'quast_strict_na': [
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140 clihelp: 'Break contigs in any misassembly event when compute NAx and NGAx. '+
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141 'By default, QUAST breaks contigs only by extensive misassemblies (not local ones). ' +
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142 "Default: ${params.quast_strict_na}",
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143 cliflag: '--strict-NA',
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144 clivalue: (params.quast_strict_na ?: '')
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145 ],
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146 'quast_x': [
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147 clihelp: 'Lower threshold for extensive misassembly size. All relocations with inconsistency ' +
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148 'less than extensive-mis-size are counted as local misassemblies. ' +
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149 "Default: ${params.quast_x}",
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150 cliflag: '-x',
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151 clivalue: (params.quast_x ?: '')
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152 ],
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153 'quast_local_mis_size': [
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154 clihelp: 'Lower threshold on local misassembly size. Local misassemblies with inconsistency ' +
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155 'less than local-mis-size are counted as (long) indels. ' +
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156 "Default: ${params.quast_local_mis_size}",
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157 cliflag: '--local-mis-size',
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158 clivalue: (params.quast_local_mis_size ?: '')
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159 ],
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160 'quast_sca_gap_size': [
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161 clihelp: 'Max allowed scaffold gap length difference. All relocations with inconsistency ' +
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162 'less than scaffold-gap-size are counted as scaffold gap misassemblies. ' +
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163 "Default: ${params.quast_sca_gap_size}",
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164 cliflag: '--scaffold-gap-max-size',
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165 clivalue: (params.quast_sca_gap_size ?: '')
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166 ],
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167 'quast_unaln_part_size': [
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168 clihelp: 'Lower threshold for detecting partially unaligned contigs. Such contig should have ' +
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169 'at least one unaligned fragment >= the threshold. ' +
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170 "Default: ${params.quast_unaln_part_size}",
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171 cliflag: '--unaligned-part-size',
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172 clivalue: (params.quast_unaln_part_size ?: '')
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173 ],
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174 'quast_skip_unaln_mis_ctgs': [
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175 clihelp: 'Do not distinguish contigs with >= 50% unaligned bases as a separate group ' +
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176 'By default, QUAST does not count misassemblies in them. ' +
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177 "Default: ${params.quast_skip_unaln_mis_ctgs}",
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178 cliflag: '--skip-unaligned-mis-contigs',
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179 clivalue: (params.quast_skip_unaln_mis_ctgs ?: '')
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180 ],
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181 'quast_fragmented': [
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182 clihelp: 'Reference genome may be fragmented into small pieces (e.g. scaffolded reference). ' +
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183 "Default: ${params.quast_fragmented}",
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184 cliflag: '--fragmented',
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185 clivalue: (params.quast_fragmented ? ' ' : '')
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186 ],
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187 'quast_frag_max_ident': [
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188 clihelp: 'Mark translocation as fake if both alignments are located no further than N bases ' +
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189 'from the ends of the reference fragments. ' +
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190 "Default: ${params.quast_frag_max_ident}",
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191 cliflag: '--fragmented-max-indent',
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192 clivalue: (params.quast_frag_max_ident ?: '')
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193 ],
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194 'quast_plots_format': [
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195 clihelp: 'Save plots in specified format [default: pdf]. ' +
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196 'Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz' +
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197 "Default: ${params.quast_plots_format}",
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198 cliflag: '--plots-format',
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199 clivalue: (params.quast_plots_format ?: '')
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200 ],
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201 ]
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202
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203 toolspecs.each {
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204 k, v -> tool.text['--' + k] = "${v.clihelp}"
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205 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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206 }
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207
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208 return tool
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209 } |
