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1 // Help text for medaka `consensus` within CPIPES.
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2
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3 def medakaconsensusHelp(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 'medakaconsensus_run': [
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12 clihelp: 'Run medaka `consensus` tool. Default: ' +
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13 (params.medakaconsensus_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 'medakaconsensus_batch_size': [
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18 clihelp: 'Inference batch size. ' +
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19 "Default: ${params.medakaconsensus_batch_size}",
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20 cliflag: '--batch_size',
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21 clivalue: (params.medakaconsensus_batch_size ?: '')
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22 ],
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23 'medakaconsensus_chunk_len': [
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24 clihelp: 'Chunk length of samples. ' +
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25 "Default: ${params.medakaconsensus_chunk_len}",
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26 cliflag: '--chunk_len',
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27 clivalue: (params.medakaconsensus_chunk_len ?: '')
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28 ],
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29 'medakaconsensus_chunk_ovlp': [
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30 clihelp: 'Overlap of chunks. ' +
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31 "Default: ${params.medakaconsensus_chunk_ovlp}",
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32 cliflag: '--chunk_ovlp',
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33 clivalue: (params.medakaconsensus_chunk_ovlp ?: '')
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34 ],
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35 'medakaconsensus_regions': [
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36 clihelp: 'Genomic regions to analyze, or a bed file. ' +
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37 "Default: ${params.medakaconsensus_regions}",
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38 cliflag: '--regions',
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39 clivalue: (params.medakaconsensus_regions ?: '')
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40 ],
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41 'medakaconsensus_model': [
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42 clihelp: 'Model to use. Can be a medaka model name or a basecaller model name ' +
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43 "suffixed with ':consensus' or ':variant'. " +
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44 "Ex: 'dna_r10.4.1_e8.2_400bps_hac@v4.1.0:variant'. " +
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45 "Default: ${params.medakaconsensus_model}",
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46 cliflag: '--model',
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47 clivalue: (params.medakaconsensus_model ?: '')
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48 ],
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49 'medakaconsensus_auto_model': [
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50 clihelp: 'Automatically choose model according to input. Use one of ' +
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51 "'consensus' or 'variant'. Default: ${params.medakaconsensus_auto_model}",
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52 cliflag: '--auto_model',
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53 clivalue: (params.medakaconsensus_auto_model ?: '')
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54 ],
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55 'medakaconsensus_bam_chunk': [
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56 clihelp: 'Size of reference chunks each worker parses from bam. ' +
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57 "Default: ${params.medakaconsensus_bam_chunk}",
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58 cliflag: '--bam_chunk',
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59 clivalue: (params.medakaconsensus_bam_chunk ?: '')
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60 ],
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61 'medakaconsensus_chk_out': [
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62 clihelp: 'Verify integrity of output file after inference. ' +
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63 "Default: ${params.medakaconsensus_chk_out}",
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64 cliflag: '--check_output',
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65 clivalue: (params.medakaconsensus_chk_out ? ' ' : '')
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66 ],
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67 'medakaconsensus_save_feats': [
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68 clihelp: 'Save features with consensus probabilities. ' +
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69 "Default: ${params.medakaconsensus_save_feats}",
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70 cliflag: '--save_features',
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71 clivalue: (params.medakaconsensus_save_feats ? ' ' : '')
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72 ],
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73 'medakaconsensus_read_grp': [
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74 clihelp: "Read group to select. Default: ${params.medakaconsensus_read_grp}",
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75 cliflag: '--RG',
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76 clivalue: (params.medakaconsensus_read_grp ?: '')
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77 ],
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78 'medakaconsensus_tag_name': [
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79 clihelp: "Two-letter tag name. Default: ${params.medakaconsensus_tag_name}",
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80 cliflag: '--tag_name',
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81 clivalue: (params.medakaconsensus_tag_name ?: '')
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82 ],
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83 'medakaconsensus_tag_val': [
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84 clihelp: "Value of tag. Default: ${params.medakaconsensus_tag_val}",
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85 cliflag: '--tag_val',
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86 clivalue: (params.medakaconsensus_tag_val ?: '')
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87 ],
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88 'medakaconsensus_tag_keep': [
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89 clihelp: 'Keep alignments when tag is missing. '
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90 + "Default: ${params.medakaconsensus_tag_keep}",
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91 cliflag: '--tag_keep_missing',
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92 clivalue: (params.medakaconsensus_tag_keep ?: '')
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93 ]
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94 ]
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95
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96 toolspecs.each {
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97 k, v -> tool.text['--' + k] = "${v.clihelp}"
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98 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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99 }
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100
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101 return tool
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102 } |
