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