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annotate 0.7.0/lib/help/kmaalign.nf @ 18:75558ffe3e68

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 11:01:13 -0400
parents 0e7a0053e4a6
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kkonganti@17 1 // Help text for kma align within CPIPES.
kkonganti@17 2
kkonganti@17 3 def kmaalignHelp(params) {
kkonganti@17 4
kkonganti@17 5 Map tool = [:]
kkonganti@17 6 Map toolspecs = [:]
kkonganti@17 7 tool.text = [:]
kkonganti@17 8 tool.helpparams = [:]
kkonganti@17 9
kkonganti@17 10 toolspecs = [
kkonganti@17 11 'kmaalign_run': [
kkonganti@17 12 clihelp: 'Run kma tool. Default: ' +
kkonganti@17 13 (params.kmaalign_run ?: false),
kkonganti@17 14 cliflag: null,
kkonganti@17 15 clivalue: null
kkonganti@17 16 ],
kkonganti@17 17 'kmaalign_int': [
kkonganti@17 18 clihelp: 'Input file has interleaved reads. ' +
kkonganti@17 19 " Default: ${params.kmaalign_int}",
kkonganti@17 20 cliflag: '-int',
kkonganti@17 21 clivalue: (params.kmaalign_int ? ' ' : '')
kkonganti@17 22 ],
kkonganti@17 23 'kmaalign_ef': [
kkonganti@17 24 clihelp: 'Output additional features. ' +
kkonganti@17 25 "Default: ${params.kmaalign_ef}",
kkonganti@17 26 cliflag: '-ef',
kkonganti@17 27 clivalue: (params.kmaalign_ef ? ' ' : '')
kkonganti@17 28 ],
kkonganti@17 29 'kmaalign_vcf': [
kkonganti@17 30 clihelp: 'Output vcf file. 2 to apply FT. ' +
kkonganti@17 31 "Default: ${params.kmaalign_vcf}",
kkonganti@17 32 cliflag: '-vcf',
kkonganti@17 33 clivalue: (params.kmaalign_vcf ? ' ' : '')
kkonganti@17 34 ],
kkonganti@17 35 'kmaalign_sam': [
kkonganti@17 36 clihelp: 'Output SAM, 4/2096 for mapped/aligned. ' +
kkonganti@17 37 "Default: ${params.kmaalign_sam}",
kkonganti@17 38 cliflag: '-sam',
kkonganti@17 39 clivalue: (params.kmaalign_sam ? ' ' : '')
kkonganti@17 40 ],
kkonganti@17 41 'kmaalign_nc': [
kkonganti@17 42 clihelp: 'No consensus file. ' +
kkonganti@17 43 "Default: ${params.kmaalign_nc}",
kkonganti@17 44 cliflag: '-nc',
kkonganti@17 45 clivalue: (params.kmaalign_nc ? ' ' : '')
kkonganti@17 46 ],
kkonganti@17 47 'kmaalign_na': [
kkonganti@17 48 clihelp: 'No aln file. ' +
kkonganti@17 49 "Default: ${params.kmaalign_na}",
kkonganti@17 50 cliflag: '-na',
kkonganti@17 51 clivalue: (params.kmaalign_na ? ' ' : '')
kkonganti@17 52 ],
kkonganti@17 53 'kmaalign_nf': [
kkonganti@17 54 clihelp: 'No frag file. ' +
kkonganti@17 55 "Default: ${params.kmaalign_nf}",
kkonganti@17 56 cliflag: '-nf',
kkonganti@17 57 clivalue: (params.kmaalign_nf ? ' ' : '')
kkonganti@17 58 ],
kkonganti@17 59 'kmaalign_a': [
kkonganti@17 60 clihelp: 'Output all template mappings. ' +
kkonganti@17 61 "Default: ${params.kmaalign_a}",
kkonganti@17 62 cliflag: '-a',
kkonganti@17 63 clivalue: (params.kmaalign_a ? ' ' : '')
kkonganti@17 64 ],
kkonganti@17 65 'kmaalign_and': [
kkonganti@17 66 clihelp: 'Use both -mrs and p-value on consensus. ' +
kkonganti@17 67 "Default: ${params.kmaalign_and}",
kkonganti@17 68 cliflag: '-and',
kkonganti@17 69 clivalue: (params.kmaalign_and ? ' ' : '')
kkonganti@17 70 ],
kkonganti@17 71 'kmaalign_oa': [
kkonganti@17 72 clihelp: 'Use neither -mrs or p-value on consensus. ' +
kkonganti@17 73 "Default: ${params.kmaalign_oa}",
kkonganti@17 74 cliflag: '-oa',
kkonganti@17 75 clivalue: (params.kmaalign_oa ? ' ' : '')
kkonganti@17 76 ],
kkonganti@17 77 'kmaalign_bc': [
kkonganti@17 78 clihelp: 'Minimum support to call bases. ' +
kkonganti@17 79 "Default: ${params.kmaalign_bc}",
kkonganti@17 80 cliflag: '-bc',
kkonganti@17 81 clivalue: (params.kmaalign_bc ?: '')
kkonganti@17 82 ],
kkonganti@17 83 'kmaalign_bcNano': [
kkonganti@17 84 clihelp: 'Altered indel calling for ONT data. ' +
kkonganti@17 85 "Default: ${params.kmaalign_bcNano}",
kkonganti@17 86 cliflag: '-bcNano',
kkonganti@17 87 clivalue: (params.kmaalign_bcNano ? ' ' : '')
kkonganti@17 88 ],
kkonganti@17 89 'kmaalign_bcd': [
kkonganti@17 90 clihelp: 'Minimum depth to call bases. ' +
kkonganti@17 91 "Default: ${params.kmaalign_bcd}",
kkonganti@17 92 cliflag: '-bcd',
kkonganti@17 93 clivalue: (params.kmaalign_bcd ?: '')
kkonganti@17 94 ],
kkonganti@17 95 'kmaalign_bcg': [
kkonganti@17 96 clihelp: 'Maintain insignificant gaps. ' +
kkonganti@17 97 "Default: ${params.kmaalign_bcg}",
kkonganti@17 98 cliflag: '-bcg',
kkonganti@17 99 clivalue: (params.kmaalign_bcg ? ' ' : '')
kkonganti@17 100 ],
kkonganti@17 101 'kmaalign_ID': [
kkonganti@17 102 clihelp: 'Minimum consensus ID. ' +
kkonganti@17 103 "Default: ${params.kmaalign_ID}",
kkonganti@17 104 cliflag: '-ID',
kkonganti@17 105 clivalue: (params.kmaalign_ID ?: '')
kkonganti@17 106 ],
kkonganti@17 107 'kmaalign_md': [
kkonganti@17 108 clihelp: 'Minimum depth. ' +
kkonganti@17 109 "Default: ${params.kmaalign_md}",
kkonganti@17 110 cliflag: '-md',
kkonganti@17 111 clivalue: (params.kmaalign_md ?: '')
kkonganti@17 112 ],
kkonganti@17 113 'kmaalign_dense': [
kkonganti@17 114 clihelp: 'Skip insertion in consensus. ' +
kkonganti@17 115 "Default: ${params.kmaalign_dense}",
kkonganti@17 116 cliflag: '-dense',
kkonganti@17 117 clivalue: (params.kmaalign_dense ? ' ' : '')
kkonganti@17 118 ],
kkonganti@17 119 'kmaalign_ref_fsa': [
kkonganti@17 120 clihelp: 'Use Ns on indels. ' +
kkonganti@17 121 "Default: ${params.kmaalign_ref_fsa}",
kkonganti@17 122 cliflag: '-ref_fsa',
kkonganti@17 123 clivalue: (params.kmaalign_ref_fsa ? ' ' : '')
kkonganti@17 124 ],
kkonganti@17 125 'kmaalign_Mt1': [
kkonganti@17 126 clihelp: 'Map everything to one template. ' +
kkonganti@17 127 "Default: ${params.kmaalign_Mt1}",
kkonganti@17 128 cliflag: '-Mt1',
kkonganti@17 129 clivalue: (params.kmaalign_Mt1 ? ' ' : '')
kkonganti@17 130 ],
kkonganti@17 131 'kmaalign_1t1': [
kkonganti@17 132 clihelp: 'Map one query to one template. ' +
kkonganti@17 133 "Default: ${params.kmaalign_1t1}",
kkonganti@17 134 cliflag: '-1t1',
kkonganti@17 135 clivalue: (params.kmaalign_1t1 ? ' ' : '')
kkonganti@17 136 ],
kkonganti@17 137 'kmaalign_mrs': [
kkonganti@17 138 clihelp: 'Minimum relative alignment score. ' +
kkonganti@17 139 "Default: ${params.kmaalign_mrs}",
kkonganti@17 140 cliflag: '-mrs',
kkonganti@17 141 clivalue: (params.kmaalign_mrs ?: '')
kkonganti@17 142 ],
kkonganti@17 143 'kmaalign_mrc': [
kkonganti@17 144 clihelp: 'Minimum query coverage. ' +
kkonganti@17 145 "Default: ${params.kmaalign_mrc}",
kkonganti@17 146 cliflag: '-mrc',
kkonganti@17 147 clivalue: (params.kmaalign_mrc ?: '')
kkonganti@17 148 ],
kkonganti@17 149 'kmaalign_mp': [
kkonganti@17 150 clihelp: 'Minimum phred score of trailing and leading bases. ' +
kkonganti@17 151 "Default: ${params.kmaalign_mp}",
kkonganti@17 152 cliflag: '-mp',
kkonganti@17 153 clivalue: (params.kmaalign_mp ?: '')
kkonganti@17 154 ],
kkonganti@17 155 'kmaalign_mq': [
kkonganti@17 156 clihelp: 'Set the minimum mapping quality. ' +
kkonganti@17 157 "Default: ${params.kmaalign_mq}",
kkonganti@17 158 cliflag: '-mq',
kkonganti@17 159 clivalue: (params.kmaalign_mq ?: '')
kkonganti@17 160 ],
kkonganti@17 161 'kmaalign_eq': [
kkonganti@17 162 clihelp: 'Minimum average quality score. ' +
kkonganti@17 163 "Default: ${params.kmaalign_eq}",
kkonganti@17 164 cliflag: '-eq',
kkonganti@17 165 clivalue: (params.kmaalign_eq ?: '')
kkonganti@17 166 ],
kkonganti@17 167 'kmaalign_5p': [
kkonganti@17 168 clihelp: 'Trim 5 prime by this many bases. ' +
kkonganti@17 169 "Default: ${params.kmaalign_5p}",
kkonganti@17 170 cliflag: '-5p',
kkonganti@17 171 clivalue: (params.kmaalign_5p ?: '')
kkonganti@17 172 ],
kkonganti@17 173 'kmaalign_3p': [
kkonganti@17 174 clihelp: 'Trim 3 prime by this many bases ' +
kkonganti@17 175 "Default: ${params.kmaalign_3p}",
kkonganti@17 176 cliflag: '-3p',
kkonganti@17 177 clivalue: (params.kmaalign_3p ?: '')
kkonganti@17 178 ],
kkonganti@17 179 'kmaalign_apm': [
kkonganti@17 180 clihelp: 'Sets both -pm and -fpm ' +
kkonganti@17 181 "Default: ${params.kmaalign_apm}",
kkonganti@17 182 cliflag: '-apm',
kkonganti@17 183 clivalue: (params.kmaalign_apm ?: '')
kkonganti@17 184 ],
kkonganti@17 185 'kmaalign_cge': [
kkonganti@17 186 clihelp: 'Set CGE penalties and rewards ' +
kkonganti@17 187 "Default: ${params.kmaalign_cge}",
kkonganti@17 188 cliflag: '-cge',
kkonganti@17 189 clivalue: (params.kmaalign_cge ? ' ' : '')
kkonganti@17 190 ],
kkonganti@17 191
kkonganti@17 192 ]
kkonganti@17 193
kkonganti@17 194 toolspecs.each {
kkonganti@17 195 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17 196 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17 197 }
kkonganti@17 198
kkonganti@17 199 return tool
kkonganti@17 200 }