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comparison 0.2.0/lib/help/bbmerge.nf @ 11:a5f31c44f8c9

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 // Help text for bbmerge within CPIPES.
2
3 def bbmergeHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'bbmerge_run': [
12 clihelp: 'Run BBMerge tool. Default: ' +
13 (params.bbmerge_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'bbmerge_reads': [
18 clihelp: 'Quit after this many read pairs (-1 means all) ' +
19 <<<<<<< HEAD
20 "Defaut: ${params.bbmerge_reads}",
21 =======
22 "Default: ${params.bbmerge_reads}",
23 >>>>>>> 0.5.0
24 cliflag: 'reads=',
25 clivalue: (params.bbmerge_reads ?: '')
26 ],
27 'bbmerge_adapters': [
28 clihelp: 'Absolute UNIX path pointing to the adapters file in ' +
29 <<<<<<< HEAD
30 "FASTA format. Defaut: ${params.bbmerge_adapters}",
31 =======
32 "FASTA format. Default: ${params.bbmerge_adapters}",
33 >>>>>>> 0.5.0
34 cliflag: 'adapters=',
35 clivalue: (params.bbmerge_adapters ?: '')
36 ],
37 'bbmerge_ziplevel': [
38 clihelp: 'Set to 1 (lowest) through 9 (max) to change compression ' +
39 "level; lower compression is faster. Default: ${params.bbmerge_ziplevel}",
40 cliflag: 'ziplevel=',
41 clivalue: (params.bbmerge_ziplevel ?: '')
42 ],
43 'bbmerge_ordered': [
44 clihelp: 'Output reads in the same order as input. ' +
45 "Default: ${params.bbmerge_ordered}",
46 cliflag: 'ordered=',
47 clivalue: (params.bbmerge_ordered ?: '')
48 ],
49 'bbmerge_qtrim': [
50 clihelp: 'Trim read ends to remove bases with quality below --bbmerge_minq. ' +
51 'Trims BEFORE merging. Values: t (trim both ends), ' +
52 'f (neither end), r (right end only), l (left end only). ' +
53 "Default: ${params.bbmerge_qtrim}",
54 cliflag: 'qtrim=',
55 clivalue: (params.bbmerge_qtrim ?: '')
56 ],
57 'bbmerge_qtrim2': [
58 clihelp: 'May be specified instead of --bbmerge_qtrim to perform trimming ' +
59 'only if merging is unsuccesful. then retry merging. ' +
60 "Default: ${params.bbmerge_qtrim2}",
61 cliflag: 'qtrim2=',
62 clivalue: (params.bbmerge_qtrim2 ?: '')
63 ],
64 'bbmerge_trimq': [
65 clihelp: 'Trim quality threshold. This may be comma-delimited list (ascending) ' +
66 "to try multiple values. Default: ${params.bbmerge_trimq}",
67 cliflag: 'trimq=',
68 clivalue: (params.bbmerge_trimq ?: '')
69 ],
70 'bbmerge_minlength': [
71 clihelp: '(ml) Reads shorter than this after trimming, but before ' +
72 'merging, will be discarded. Pairs will be discarded only' +
73 "if both are shorter. Default: ${params.bbmerge_minlength}",
74 cliflag: 'minlength=',
75 clivalue: (params.bbmerge_minlength ?: '')
76 ],
77 'bbmerge_tbo': [
78 clihelp: '(trimbyoverlap). Trim overlapping reads to remove right ' +
79 "most (3') non-overlaping portion instead of joining " +
80 "Default: ${params.bbmerge_tbo}",
81 cliflag: 'tbo=',
82 clivalue: (params.bbmerge_tbo ?: '')
83 ],
84 'bbmerge_minavgquality': [
85 clihelp: '(maq). Reads with average quality below this after trimming will ' +
86 "not be attempted to merge. Default: ${params.bbmerge_minavgquality}",
87 cliflag: 'minavgquality=',
88 clivalue: (params.bbmerge_minavgquality ?: '')
89 ],
90 'bbmerge_trimpolya': [
91 clihelp: 'Trim trailing poly-A tail from adapter output. Only affects ' +
92 'outadapter. This also trims poly-A followed by poly-G, which ' +
93 "occurs on NextSeq. Default: ${params.bbmerge_trimpolya}",
94 cliflag: 'trimpolya=',
95 clivalue: (params.bbmerge_trimpolya ?: '')
96 ],
97 'bbmerge_pfilter': [
98 clihelp: 'Ban improbable overlaps. Higher is more strict. 0 will ' +
99 'disable the filter; 1 will allow only perfect overlaps. ' +
100 "Default: ${params.bbmerge_pfilter}",
101 cliflag: 'pfilter=',
102 clivalue: (params.bbmerge_pfilter ?: '')
103 ],
104 'bbmerge_ouq': [
105 clihelp: 'Calculate best overlap using quality values. ' +
106 "Default: ${params.bbmerge_ouq}",
107 cliflag: 'ouq',
108 clivalue: (params.bbmerge_ouq ?: '')
109 ],
110 'bbmerge_owq': [
111 clihelp: 'Calculate best overlap without using quality values. ' +
112 "Default: ${params.bbmerge_owq}",
113 cliflag: 'owq=',
114 clivalue: (params.bbmerge_owq ?: '')
115 ],
116 'bbmerge_strict': [
117 clihelp: 'Decrease false positive rate and merging rate. ' +
118 "Default: ${params.bbmerge_strict}",
119 cliflag: 'strict=',
120 clivalue: (params.bbmerge_strict ?: '')
121 ],
122 'bbmerge_verystrict': [
123 clihelp: 'Greatly decrease false positive rate and merging rate. ' +
124 "Default: ${params.bbmerge_verystrict}",
125 cliflag: 'verystrict=',
126 clivalue: (params.bbmerge_verystrict ?: '')
127 ],
128 'bbmerge_ultrastrict': [
129 clihelp: 'Decrease false positive rate and merging rate even more. ' +
130 "Default: ${params.bbmerge_ultrastrict}",
131 cliflag: 'ultrastrict=',
132 clivalue: (params.bbmerge_ultrastrict ?: '')
133 ],
134 'bbmerge_maxstrict': [
135 clihelp: 'Maxiamally decrease false positive rate and merging rate. ' +
136 "Default: ${params.bbmerge_maxstrict}",
137 cliflag: 'maxstrict=',
138 clivalue: (params.bbmerge_maxstrict ?: '')
139 ],
140 'bbmerge_loose': [
141 clihelp: 'Increase false positive rate and merging rate. ' +
142 "Default: ${params.bbmerge_loose}",
143 cliflag: 'loose=',
144 clivalue: (params.bbmerge_loose ?: '')
145 ],
146 'bbmerge_veryloose': [
147 clihelp: 'Greatly increase false positive rate and merging rate. ' +
148 "Default: ${params.bbmerge_veryloose}",
149 cliflag: 'veryloose=',
150 clivalue: (params.bbmerge_veryloose ?: '')
151 ],
152 'bbmerge_ultraloose': [
153 clihelp: 'Increase false positive rate and merging rate even more. ' +
154 "Default: ${params.bbmerge_ultraloose}",
155 cliflag: 'ultraloose=',
156 clivalue: (params.bbmerge_ultraloose ?: '')
157 ],
158 'bbmerge_maxloose': [
159 clihelp: 'Maximally increase false positive rate and merging rate. ' +
160 "Default: ${params.bbmerge_maxloose}",
161 cliflag: 'maxloose=',
162 clivalue: (params.bbmerge_maxloose ?: '')
163 ],
164 'bbmerge_fast': [
165 clihelp: 'Fastest possible preset. ' +
166 "Default: ${params.bbmerge_fast}",
167 cliflag: 'fast=',
168 clivalue: (params.bbmerge_fast ?: '')
169 ],
170 'bbmerge_k': [
171 clihelp: 'Kmer length. 31 (or less) is fastest and uses the least ' +
172 'memory, but higher values may be more accurate. ' +
173 '60 tends to work well for 150bp reads. ' +
174 "Default: ${params.bbmerge_k}",
175 cliflag: 'k=',
176 clivalue: (params.bbmerge_k ?: '')
177 ],
178 'bbmerge_prealloc': [
179 clihelp: 'Pre-allocate memory rather than dynamically growing. ' +
180 'Faster and more memory-efficient for large datasets. ' +
181 'A float fraction (0-1) may be specified, default 1. ' +
182 "Default: ${params.bbmerge_prealloc}",
183 cliflag: 'prealloc=',
184 clivalue: (params.bbmerge_prealloc ?: '')
185 ]
186 ]
187
188 toolspecs.each {
189 k, v -> tool.text['--' + k] = "${v.clihelp}"
190 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
191 }
192
193 return tool
194 }