|
0
|
1 // Help text for filtlong within CPIPES.
|
|
|
2
|
|
|
3 def filtlongHelp(params) {
|
|
|
4
|
|
|
5 Map tool = [:]
|
|
|
6 Map toolspecs = [:]
|
|
|
7 tool.text = [:]
|
|
|
8 tool.helpparams = [:]
|
|
|
9
|
|
|
10 toolspecs = [
|
|
|
11 'filtlong_run': [
|
|
|
12 clihelp: 'Run filtlong read trimming tool. Default: ' +
|
|
|
13 (params.filtlong_run ?: false),
|
|
|
14 cliflag: null,
|
|
|
15 clivalue: null
|
|
|
16 ],
|
|
|
17 'filtlong_keep_perc': [
|
|
|
18 clihelp: 'Keep only this percentage of best reads. ' +
|
|
|
19 "Default: ${params.filtlong_keep_perc}",
|
|
|
20 cliflag: '--keep_percent',
|
|
|
21 clivalue: (params.filtlong_keep_perc ?: '')
|
|
|
22 ],
|
|
|
23 'filtlong_target_bases': [
|
|
|
24 clihelp: 'Keep only the best bases up to this many total bases. ' +
|
|
|
25 "Default: ${params.filtlong_target_bases}",
|
|
|
26 cliflag: '--target_bases',
|
|
|
27 clivalue: (params.filtlong_target_bases ?: '')
|
|
|
28 ],
|
|
|
29 'filtlong_min_length': [
|
|
|
30 clihelp: 'Minimum length threshold. ' +
|
|
|
31 "Default: ${params.filtlong_min_length}",
|
|
|
32 cliflag: '--min_length',
|
|
|
33 clivalue: (params.filtlong_min_length ?: '')
|
|
|
34 ],
|
|
|
35 'filtlong_max_length': [
|
|
|
36 clihelp: 'Maximum length threshold. ' +
|
|
|
37 "Default: ${params.filtlong_max_length}",
|
|
|
38 cliflag: '--max_length',
|
|
|
39 clivalue: (params.filtlong_max_length ?: '')
|
|
|
40 ],
|
|
|
41 'filtlong_min_mean_q': [
|
|
|
42 clihelp: 'Minimum mean quality threshold. ' +
|
|
|
43 "Default: ${params.filtlong_min_mean_q}",
|
|
|
44 cliflag: '--min_mean_q',
|
|
|
45 clivalue: (params.filtlong_min_mean_q ?: '')
|
|
|
46 ],
|
|
|
47 'filtlong_min_window_q': [
|
|
|
48 clihelp: 'Minimum window quality threshold. ' +
|
|
|
49 "Default: ${params.filtlong_min_window_q}",
|
|
|
50 cliflag: '--min_window_q',
|
|
|
51 clivalue: (params.filtlong_min_window_q ?: '')
|
|
|
52 ],
|
|
|
53 'filtlong_a': [
|
|
|
54 clihelp: "External reference assembly in FASTA format. " +
|
|
|
55 "Default: ${params.filtlong_a}",
|
|
|
56 cliflag: '-a',
|
|
|
57 clivalue: (params.filtlong_a ?: '')
|
|
|
58 ],
|
|
|
59 'filtlong_1': [
|
|
|
60 clihelp: 'External reference Illumina reads in FASTQ format (R1). ' +
|
|
|
61 "Default: ${params.filtlong_1}",
|
|
|
62 cliflag: '-1',
|
|
|
63 clivalue: (params.filtlong_1 ?: '')
|
|
|
64 ],
|
|
|
65 'filtlong_2': [
|
|
|
66 clihelp: 'External reference Illumina reads in FASTQ format (R2). ' +
|
|
|
67 "Default: ${params.filtlong_2}",
|
|
|
68 cliflag: '--2',
|
|
|
69 clivalue: (params.filtlong_2 ?: '')
|
|
|
70 ],
|
|
|
71 'filtlong_len_weight': [
|
|
|
72 clihelp: 'Weight given to the length score. ' +
|
|
|
73 "Default: ${params.filtlong_len_weight}",
|
|
|
74 cliflag: '--length_weight',
|
|
|
75 clivalue: (params.filtlong_len_weight ?: '')
|
|
|
76 ],
|
|
|
77 'filtlong_mean_q_weight': [
|
|
|
78 clihelp: 'Weight given to the mean quality score. ' +
|
|
|
79 "Default: ${params.filtlong_mean_q_weight}",
|
|
|
80 cliflag: '--mean_q_weight',
|
|
|
81 clivalue: (params.filtlong_mean_q_weight ?: '')
|
|
|
82 ],
|
|
|
83 'filtlong_window_q_weight': [
|
|
|
84 clihelp: 'Weight given to the window quality score. ' +
|
|
|
85 "Default: ${params.filtlong_window_q_weight}",
|
|
|
86 cliflag: '--window_q_weight',
|
|
|
87 clivalue: (params.filtlong_window_q_weight ?: '')
|
|
|
88 ],
|
|
|
89 'filtlong_trim': [
|
|
|
90 clihelp: 'Trim non k-mer matching bases from start/end of the reads. ' +
|
|
|
91 "Default: ${params.filtlong_trim}",
|
|
|
92 cliflag: '--trim',
|
|
|
93 clivalue: (params.filtlong_trim ? ' ' : '')
|
|
|
94 ],
|
|
|
95 'filtlong_split': [
|
|
|
96 clihelp: 'Split reads at this many (or more) consecutive non k-mer matching bases. ' +
|
|
|
97 "Default: ${params.filtlong_split}",
|
|
|
98 cliflag: '--split',
|
|
|
99 clivalue: (params.filtlong_split ? ' ' : '')
|
|
|
100 ],
|
|
|
101 'filtlong_window_size': [
|
|
|
102 clihelp: 'Size of sliding window used when measuring window quality. ' +
|
|
|
103 "Default: ${params.filtlong_window_size}",
|
|
|
104 cliflag: '--window_size',
|
|
|
105 clivalue: (params.filtlong_window_size ?: '')
|
|
|
106 ]
|
|
|
107 ]
|
|
|
108
|
|
|
109 toolspecs.each {
|
|
|
110 k, v -> tool.text['--' + k] = "${v.clihelp}"
|
|
|
111 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
|
|
|
112 }
|
|
|
113
|
|
|
114 return tool
|
|
|
115 } |
