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annotate 0.5.0/lib/help/kmaalign.nf @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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kkonganti@0 1 // Help text for kma align within CPIPES.
kkonganti@0 2
kkonganti@0 3 def kmaalignHelp(params) {
kkonganti@0 4
kkonganti@0 5 Map tool = [:]
kkonganti@0 6 Map toolspecs = [:]
kkonganti@0 7 tool.text = [:]
kkonganti@0 8 tool.helpparams = [:]
kkonganti@0 9
kkonganti@0 10 toolspecs = [
kkonganti@0 11 'kmaalign_run': [
kkonganti@0 12 clihelp: 'Run kma tool. Default: ' +
kkonganti@0 13 (params.kmaalign_run ?: false),
kkonganti@0 14 cliflag: null,
kkonganti@0 15 clivalue: null
kkonganti@0 16 ],
kkonganti@0 17 'kmaalign_int': [
kkonganti@0 18 clihelp: 'Input file has interleaved reads. ' +
kkonganti@0 19 " Default: ${params.kmaalign_int}",
kkonganti@0 20 cliflag: '-int',
kkonganti@0 21 clivalue: (params.kmaalign_int ? ' ' : '')
kkonganti@0 22 ],
kkonganti@0 23 'kmaalign_ef': [
kkonganti@0 24 clihelp: 'Output additional features. ' +
kkonganti@0 25 "Default: ${params.kmaalign_ef}",
kkonganti@0 26 cliflag: '-ef',
kkonganti@0 27 clivalue: (params.kmaalign_ef ? ' ' : '')
kkonganti@0 28 ],
kkonganti@0 29 'kmaalign_vcf': [
kkonganti@0 30 clihelp: 'Output vcf file. 2 to apply FT. ' +
kkonganti@0 31 "Default: ${params.kmaalign_vcf}",
kkonganti@0 32 cliflag: '-vcf',
kkonganti@0 33 clivalue: (params.kmaalign_vcf ? ' ' : '')
kkonganti@0 34 ],
kkonganti@0 35 'kmaalign_sam': [
kkonganti@0 36 clihelp: 'Output SAM, 4/2096 for mapped/aligned. ' +
kkonganti@0 37 "Default: ${params.kmaalign_sam}",
kkonganti@0 38 cliflag: '-sam',
kkonganti@0 39 clivalue: (params.kmaalign_sam ? ' ' : '')
kkonganti@0 40 ],
kkonganti@0 41 'kmaalign_nc': [
kkonganti@0 42 clihelp: 'No consensus file. ' +
kkonganti@0 43 "Default: ${params.kmaalign_nc}",
kkonganti@0 44 cliflag: '-nc',
kkonganti@0 45 clivalue: (params.kmaalign_nc ? ' ' : '')
kkonganti@0 46 ],
kkonganti@0 47 'kmaalign_na': [
kkonganti@0 48 clihelp: 'No aln file. ' +
kkonganti@0 49 "Default: ${params.kmaalign_na}",
kkonganti@0 50 cliflag: '-na',
kkonganti@0 51 clivalue: (params.kmaalign_na ? ' ' : '')
kkonganti@0 52 ],
kkonganti@0 53 'kmaalign_nf': [
kkonganti@0 54 clihelp: 'No frag file. ' +
kkonganti@0 55 "Default: ${params.kmaalign_nf}",
kkonganti@0 56 cliflag: '-nf',
kkonganti@0 57 clivalue: (params.kmaalign_nf ? ' ' : '')
kkonganti@0 58 ],
kkonganti@0 59 'kmaalign_a': [
kkonganti@0 60 clihelp: 'Output all template mappings. ' +
kkonganti@0 61 "Default: ${params.kmaalign_a}",
kkonganti@0 62 cliflag: '-a',
kkonganti@0 63 clivalue: (params.kmaalign_a ? ' ' : '')
kkonganti@0 64 ],
kkonganti@0 65 'kmaalign_and': [
kkonganti@0 66 clihelp: 'Use both -mrs and p-value on consensus. ' +
kkonganti@0 67 "Default: ${params.kmaalign_and}",
kkonganti@0 68 cliflag: '-and',
kkonganti@0 69 clivalue: (params.kmaalign_and ? ' ' : '')
kkonganti@0 70 ],
kkonganti@0 71 'kmaalign_oa': [
kkonganti@0 72 clihelp: 'Use neither -mrs or p-value on consensus. ' +
kkonganti@0 73 "Default: ${params.kmaalign_oa}",
kkonganti@0 74 cliflag: '-oa',
kkonganti@0 75 clivalue: (params.kmaalign_oa ? ' ' : '')
kkonganti@0 76 ],
kkonganti@0 77 'kmaalign_bc': [
kkonganti@0 78 clihelp: 'Minimum support to call bases. ' +
kkonganti@0 79 "Default: ${params.kmaalign_bc}",
kkonganti@0 80 cliflag: '-bc',
kkonganti@0 81 clivalue: (params.kmaalign_bc ?: '')
kkonganti@0 82 ],
kkonganti@0 83 'kmaalign_bcNano': [
kkonganti@0 84 clihelp: 'Altered indel calling for ONT data. ' +
kkonganti@0 85 "Default: ${params.kmaalign_bcNano}",
kkonganti@0 86 cliflag: '-bcNano',
kkonganti@0 87 clivalue: (params.kmaalign_bcNano ? ' ' : '')
kkonganti@0 88 ],
kkonganti@0 89 'kmaalign_bcd': [
kkonganti@0 90 clihelp: 'Minimum depth to call bases. ' +
kkonganti@0 91 "Default: ${params.kmaalign_bcd}",
kkonganti@0 92 cliflag: '-bcd',
kkonganti@0 93 clivalue: (params.kmaalign_bcd ?: '')
kkonganti@0 94 ],
kkonganti@0 95 'kmaalign_bcg': [
kkonganti@0 96 clihelp: 'Maintain insignificant gaps. ' +
kkonganti@0 97 "Default: ${params.kmaalign_bcg}",
kkonganti@0 98 cliflag: '-bcg',
kkonganti@0 99 clivalue: (params.kmaalign_bcg ? ' ' : '')
kkonganti@0 100 ],
kkonganti@0 101 'kmaalign_ID': [
kkonganti@0 102 clihelp: 'Minimum consensus ID. ' +
kkonganti@0 103 "Default: ${params.kmaalign_ID}",
kkonganti@0 104 cliflag: '-ID',
kkonganti@0 105 clivalue: (params.kmaalign_ID ?: '')
kkonganti@0 106 ],
kkonganti@0 107 'kmaalign_md': [
kkonganti@0 108 clihelp: 'Minimum depth. ' +
kkonganti@0 109 "Default: ${params.kmaalign_md}",
kkonganti@0 110 cliflag: '-md',
kkonganti@0 111 clivalue: (params.kmaalign_md ?: '')
kkonganti@0 112 ],
kkonganti@0 113 'kmaalign_dense': [
kkonganti@0 114 clihelp: 'Skip insertion in consensus. ' +
kkonganti@0 115 "Default: ${params.kmaalign_dense}",
kkonganti@0 116 cliflag: '-dense',
kkonganti@0 117 clivalue: (params.kmaalign_dense ? ' ' : '')
kkonganti@0 118 ],
kkonganti@0 119 'kmaalign_ref_fsa': [
kkonganti@0 120 clihelp: 'Use Ns on indels. ' +
kkonganti@0 121 "Default: ${params.kmaalign_ref_fsa}",
kkonganti@0 122 cliflag: '-ref_fsa',
kkonganti@0 123 clivalue: (params.kmaalign_ref_fsa ? ' ' : '')
kkonganti@0 124 ],
kkonganti@0 125 'kmaalign_Mt1': [
kkonganti@0 126 clihelp: 'Map everything to one template. ' +
kkonganti@0 127 "Default: ${params.kmaalign_Mt1}",
kkonganti@0 128 cliflag: '-Mt1',
kkonganti@0 129 clivalue: (params.kmaalign_Mt1 ? ' ' : '')
kkonganti@0 130 ],
kkonganti@0 131 'kmaalign_1t1': [
kkonganti@0 132 clihelp: 'Map one query to one template. ' +
kkonganti@0 133 "Default: ${params.kmaalign_1t1}",
kkonganti@0 134 cliflag: '-1t1',
kkonganti@0 135 clivalue: (params.kmaalign_1t1 ? ' ' : '')
kkonganti@0 136 ],
kkonganti@0 137 'kmaalign_mrs': [
kkonganti@0 138 clihelp: 'Minimum relative alignment score. ' +
kkonganti@0 139 "Default: ${params.kmaalign_mrs}",
kkonganti@0 140 cliflag: '-mrs',
kkonganti@0 141 clivalue: (params.kmaalign_mrs ?: '')
kkonganti@0 142 ],
kkonganti@0 143 'kmaalign_mrc': [
kkonganti@0 144 clihelp: 'Minimum query coverage. ' +
kkonganti@0 145 "Default: ${params.kmaalign_mrc}",
kkonganti@0 146 cliflag: '-mrc',
kkonganti@0 147 clivalue: (params.kmaalign_mrc ?: '')
kkonganti@0 148 ],
kkonganti@0 149 'kmaalign_mp': [
kkonganti@0 150 clihelp: 'Minimum phred score of trailing and leading bases. ' +
kkonganti@0 151 "Default: ${params.kmaalign_mp}",
kkonganti@0 152 cliflag: '-mp',
kkonganti@0 153 clivalue: (params.kmaalign_mp ?: '')
kkonganti@0 154 ],
kkonganti@0 155 'kmaalign_mq': [
kkonganti@0 156 clihelp: 'Set the minimum mapping quality. ' +
kkonganti@0 157 "Default: ${params.kmaalign_mq}",
kkonganti@0 158 cliflag: '-mq',
kkonganti@0 159 clivalue: (params.kmaalign_mq ?: '')
kkonganti@0 160 ],
kkonganti@0 161 'kmaalign_eq': [
kkonganti@0 162 clihelp: 'Minimum average quality score. ' +
kkonganti@0 163 "Default: ${params.kmaalign_eq}",
kkonganti@0 164 cliflag: '-eq',
kkonganti@0 165 clivalue: (params.kmaalign_eq ?: '')
kkonganti@0 166 ],
kkonganti@0 167 'kmaalign_5p': [
kkonganti@0 168 clihelp: 'Trim 5 prime by this many bases. ' +
kkonganti@0 169 "Default: ${params.kmaalign_5p}",
kkonganti@0 170 cliflag: '-5p',
kkonganti@0 171 clivalue: (params.kmaalign_5p ?: '')
kkonganti@0 172 ],
kkonganti@0 173 'kmaalign_3p': [
kkonganti@0 174 clihelp: 'Trim 3 prime by this many bases ' +
kkonganti@0 175 "Default: ${params.kmaalign_3p}",
kkonganti@0 176 cliflag: '-3p',
kkonganti@0 177 clivalue: (params.kmaalign_3p ?: '')
kkonganti@0 178 ],
kkonganti@0 179 'kmaalign_apm': [
kkonganti@0 180 clihelp: 'Sets both -pm and -fpm ' +
kkonganti@0 181 "Default: ${params.kmaalign_apm}",
kkonganti@0 182 cliflag: '-apm',
kkonganti@0 183 clivalue: (params.kmaalign_apm ?: '')
kkonganti@0 184 ],
kkonganti@0 185 'kmaalign_cge': [
kkonganti@0 186 clihelp: 'Set CGE penalties and rewards ' +
kkonganti@0 187 "Default: ${params.kmaalign_cge}",
kkonganti@0 188 cliflag: '-cge',
kkonganti@0 189 clivalue: (params.kmaalign_cge ? ' ' : '')
kkonganti@0 190 ],
kkonganti@0 191
kkonganti@0 192 ]
kkonganti@0 193
kkonganti@0 194 toolspecs.each {
kkonganti@0 195 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0 196 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0 197 }
kkonganti@0 198
kkonganti@0 199 return tool
kkonganti@0 200 }