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comparison 0.2.0/lib/help/kmaalign.nf @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 // Help text for kma align within CPIPES.
2
3 def kmaalignHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'kmaalign_run': [
12 clihelp: 'Run kma tool. Default: ' +
13 (params.kmaalign_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'kmaalign_int': [
18 clihelp: 'Input file has interleaved reads. ' +
19 " Default: ${params.kmaalign_int}",
20 cliflag: '-int',
21 clivalue: (params.kmaalign_int ? ' ' : '')
22 ],
23 'kmaalign_ef': [
24 clihelp: 'Output additional features. ' +
25 "Default: ${params.kmaalign_ef}",
26 cliflag: '-ef',
27 clivalue: (params.kmaalign_ef ? ' ' : '')
28 ],
29 'kmaalign_vcf': [
30 clihelp: 'Output vcf file. 2 to apply FT. ' +
31 "Default: ${params.kmaalign_vcf}",
32 cliflag: '-vcf',
33 clivalue: (params.kmaalign_vcf ? ' ' : '')
34 ],
35 'kmaalign_sam': [
36 clihelp: 'Output SAM, 4/2096 for mapped/aligned. ' +
37 "Default: ${params.kmaalign_sam}",
38 cliflag: '-sam',
39 clivalue: (params.kmaalign_sam ? ' ' : '')
40 ],
41 'kmaalign_nc': [
42 clihelp: 'No consensus file. ' +
43 "Default: ${params.kmaalign_nc}",
44 cliflag: '-nc',
45 clivalue: (params.kmaalign_nc ? ' ' : '')
46 ],
47 'kmaalign_na': [
48 clihelp: 'No aln file. ' +
49 "Default: ${params.kmaalign_na}",
50 cliflag: '-na',
51 clivalue: (params.kmaalign_na ? ' ' : '')
52 ],
53 'kmaalign_nf': [
54 clihelp: 'No frag file. ' +
55 "Default: ${params.kmaalign_nf}",
56 cliflag: '-nf',
57 clivalue: (params.kmaalign_nf ? ' ' : '')
58 ],
59 'kmaalign_a': [
60 clihelp: 'Output all template mappings. ' +
61 "Default: ${params.kmaalign_a}",
62 cliflag: '-a',
63 clivalue: (params.kmaalign_a ? ' ' : '')
64 ],
65 'kmaalign_and': [
66 clihelp: 'Use both -mrs and p-value on consensus. ' +
67 "Default: ${params.kmaalign_and}",
68 cliflag: '-and',
69 clivalue: (params.kmaalign_and ? ' ' : '')
70 ],
71 'kmaalign_oa': [
72 clihelp: 'Use neither -mrs or p-value on consensus. ' +
73 "Default: ${params.kmaalign_oa}",
74 cliflag: '-oa',
75 clivalue: (params.kmaalign_oa ? ' ' : '')
76 ],
77 'kmaalign_bc': [
78 clihelp: 'Minimum support to call bases. ' +
79 "Default: ${params.kmaalign_bc}",
80 cliflag: '-bc',
81 clivalue: (params.kmaalign_bc ?: '')
82 ],
83 'kmaalign_bcNano': [
84 clihelp: 'Altered indel calling for ONT data. ' +
85 "Default: ${params.kmaalign_bcNano}",
86 cliflag: '-bcNano',
87 clivalue: (params.kmaalign_bcNano ? ' ' : '')
88 ],
89 'kmaalign_bcd': [
90 clihelp: 'Minimum depth to call bases. ' +
91 "Default: ${params.kmaalign_bcd}",
92 cliflag: '-bcd',
93 clivalue: (params.kmaalign_bcd ?: '')
94 ],
95 'kmaalign_bcg': [
96 clihelp: 'Maintain insignificant gaps. ' +
97 "Default: ${params.kmaalign_bcg}",
98 cliflag: '-bcg',
99 clivalue: (params.kmaalign_bcg ? ' ' : '')
100 ],
101 'kmaalign_ID': [
102 clihelp: 'Minimum consensus ID. ' +
103 "Default: ${params.kmaalign_ID}",
104 cliflag: '-ID',
105 clivalue: (params.kmaalign_ID ?: '')
106 ],
107 'kmaalign_md': [
108 clihelp: 'Minimum depth. ' +
109 "Default: ${params.kmaalign_md}",
110 cliflag: '-md',
111 clivalue: (params.kmaalign_md ?: '')
112 ],
113 'kmaalign_dense': [
114 clihelp: 'Skip insertion in consensus. ' +
115 "Default: ${params.kmaalign_dense}",
116 cliflag: '-dense',
117 clivalue: (params.kmaalign_dense ? ' ' : '')
118 ],
119 'kmaalign_ref_fsa': [
120 clihelp: 'Use Ns on indels. ' +
121 "Default: ${params.kmaalign_ref_fsa}",
122 cliflag: '-ref_fsa',
123 clivalue: (params.kmaalign_ref_fsa ? ' ' : '')
124 ],
125 'kmaalign_Mt1': [
126 clihelp: 'Map everything to one template. ' +
127 "Default: ${params.kmaalign_Mt1}",
128 cliflag: '-Mt1',
129 clivalue: (params.kmaalign_Mt1 ? ' ' : '')
130 ],
131 'kmaalign_1t1': [
132 clihelp: 'Map one query to one template. ' +
133 "Default: ${params.kmaalign_1t1}",
134 cliflag: '-1t1',
135 clivalue: (params.kmaalign_1t1 ? ' ' : '')
136 ],
137 'kmaalign_mrs': [
138 clihelp: 'Minimum relative alignment score. ' +
139 "Default: ${params.kmaalign_mrs}",
140 cliflag: '-mrs',
141 clivalue: (params.kmaalign_mrs ?: '')
142 ],
143 'kmaalign_mrc': [
144 clihelp: 'Minimum query coverage. ' +
145 "Default: ${params.kmaalign_mrc}",
146 cliflag: '-mrc',
147 clivalue: (params.kmaalign_mrc ?: '')
148 ],
149 'kmaalign_mp': [
150 clihelp: 'Minimum phred score of trailing and leading bases. ' +
151 "Default: ${params.kmaalign_mp}",
152 cliflag: '-mp',
153 clivalue: (params.kmaalign_mp ?: '')
154 ],
155 'kmaalign_mq': [
156 clihelp: 'Set the minimum mapping quality. ' +
157 "Default: ${params.kmaalign_mq}",
158 cliflag: '-mq',
159 clivalue: (params.kmaalign_mq ?: '')
160 ],
161 'kmaalign_eq': [
162 clihelp: 'Minimum average quality score. ' +
163 "Default: ${params.kmaalign_eq}",
164 cliflag: '-eq',
165 clivalue: (params.kmaalign_eq ?: '')
166 ],
167 'kmaalign_5p': [
168 clihelp: 'Trim 5 prime by this many bases. ' +
169 "Default: ${params.kmaalign_5p}",
170 cliflag: '-5p',
171 clivalue: (params.kmaalign_5p ?: '')
172 ],
173 'kmaalign_3p': [
174 clihelp: 'Trim 3 prime by this many bases ' +
175 "Default: ${params.kmaalign_3p}",
176 cliflag: '-3p',
177 clivalue: (params.kmaalign_3p ?: '')
178 ],
179 'kmaalign_apm': [
180 clihelp: 'Sets both -pm and -fpm ' +
181 "Default: ${params.kmaalign_apm}",
182 cliflag: '-apm',
183 clivalue: (params.kmaalign_apm ?: '')
184 ],
185 'kmaalign_cge': [
186 clihelp: 'Set CGE penalties and rewards ' +
187 "Default: ${params.kmaalign_cge}",
188 cliflag: '-cge',
189 clivalue: (params.kmaalign_cge ? ' ' : '')
190 ],
191
192 ]
193
194 toolspecs.each {
195 k, v -> tool.text['--' + k] = "${v.clihelp}"
196 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
197 }
198
199 return tool
200 }