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comparison 1.0.0/lib/help/nanoplot.nf @ 0:0a8dda29956e draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 // Help text for NanoPlot within CPIPES.
2
3 def nanoplotHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'nanoplot_run': [
12 clihelp: 'Run NanoPlot tool on ONT reads. Default: ' +
13 (params.nanoplot_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'nanoplot_store': [
18 clihelp: 'Store the extracted data in a pickle file for future plotting. ' +
19 "Default: ${params.nanoplot_store}",
20 cliflag: '--store',
21 clivalue: (params.nanoplot_store ? ' ' : '')
22 ],
23 'nanoplot_raw': [
24 clihelp: 'Store the extracted data in tab separated file. ' +
25 "Default: ${params.nanoplot_raw}",
26 cliflag: '--raw',
27 clivalue: (params.nanoplot_raw ? ' ' : '')
28 ],
29 'nanoplot_huge': [
30 clihelp: 'Input data is one very large file. ' +
31 "Default: ${params.nanoplot_huge}",
32 cliflag: '--huge',
33 clivalue: (params.nanoplot_huge ? ' ' : '')
34 ],
35 'nanoplot_no_static': [
36 clihelp: 'Do not make static (png) plots. ' +
37 "Default: ${params.nanoplot_no_static}",
38 cliflag: '--no_static',
39 clivalue: (params.nanoplot_no_static ? ' ' : '')
40 ],
41 'nanoplot_tsv_stats': [
42 clihelp: 'Output the stats file as a properly formatted TSV. ' +
43 "Default: ${params.nanoplot_tsv_stats}",
44 cliflag: '--tsv_stats',
45 clivalue: (params.nanoplot_tsv_stats ? ' ' : '')
46 ],
47 'nanoplot_only_report': [
48 clihelp: 'Output only the report. ' +
49 "Default: ${params.nanoplot_only_report}",
50 cliflag: '--only-report',
51 clivalue: (params.nanoplot_only_report ? ' ' : '')
52 ],
53 'nanoplot_minlength': [
54 clihelp: "Hide reads shorter than length specified. " +
55 "Default: ${params.nanoplot_minlength}",
56 cliflag: '--minlength',
57 clivalue: (params.nanoplot_minlength ?: '')
58 ],
59 'nanoplot_maxlength': [
60 clihelp: 'Hide reads longer than length specified. ' +
61 "Default: ${params.nanoplot_maxlength}",
62 cliflag: '--maxlength',
63 clivalue: (params.nanoplot_maxlength ?: '')
64 ],
65 'nanoplot_downsample': [
66 clihelp: 'Reduce dataset to N reads by random sampling. ' +
67 "Default: ${params.nanoplot_downsample}",
68 cliflag: '--downsample',
69 clivalue: (params.nanoplot_downsample ?: '')
70 ],
71 'nanoplot_drop_outliers': [
72 clihelp: 'Drop outlier reads with extreme long length. ' +
73 "Default: ${params.nanoplot_drop_outliers}",
74 cliflag: '--drop_outliers',
75 clivalue: (params.nanoplot_drop_outliers ? ' ' : '')
76 ],
77 'nanoplot_loglength': [
78 clihelp: 'Additionally show logarithmic scaling of lengths in plots. ' +
79 "Default: ${params.nanoplot_loglength}",
80 cliflag: '--loglength',
81 clivalue: (params.nanoplot_loglength ?: '')
82 ],
83 'nanoplot_perc_qual': [
84 clihelp: 'Weight given to the window quality score. ' +
85 "Default: ${params.nanoplot_perc_qual}",
86 cliflag: '--percentqual',
87 clivalue: (params.nanoplot_perc_qual ? ' ' : '')
88 ],
89 'nanoplot_alength': [
90 clihelp: 'Use aligned read lengths rather than sequenced length (bam mode). ' +
91 "Default: ${params.nanoplot_alength}",
92 cliflag: '--alength',
93 clivalue: (params.nanoplot_alength ? ' ' : '')
94 ],
95 'nanoplot_minqual': [
96 clihelp: 'Drop reads with an average quality lower than specified. ' +
97 "Default: ${params.nanoplot_minqual}",
98 cliflag: '--minqual',
99 clivalue: (params.nanoplot_minqual ?: '')
100 ],
101 'nanoplot_runtime_until': [
102 clihelp: 'Only tke the N first hours of a run. ' +
103 "Default: ${params.nanoplot_runtime_until}",
104 cliflag: '--runtime_until',
105 clivalue: (params.nanoplot_runtime_until ?: '')
106 ],
107 'nanoplot_readtype': [
108 clihelp: 'Which read type to extract information about from summary. ' +
109 'Options are 1D, 2D, 1D2. ' +
110 "Default: ${params.nanoplot_readtype}",
111 cliflag: '--readtype',
112 clivalue: (params.nanoplot_readtype ?: '')
113 ],
114 'nanoplot_barcoded': [
115 clihelp: 'Split the summary file by barcode. ' +
116 "Default: ${params.nanoplot_barcoded}",
117 cliflag: '--barcoded',
118 clivalue: (params.nanoplot_barcoded ? ' ' : '')
119 ],
120 'nanoplot_no_supp': [
121 clihelp: 'Remove supplementary alignments. ' +
122 "Default: ${params.nanoplot_no_supp}",
123 cliflag: '--no_supplementary',
124 clivalue: (params.nanoplot_no_supp ? ' ' : '')
125 ],
126 'nanoplot_c': [
127 clihelp: 'Specify a valid matplotlib color for the plots. ' +
128 "Default: ${params.nanoplot_c}",
129 cliflag: '-c',
130 clivalue: (params.nanoplot_c ?: '')
131 ],
132 'nanoplot_cm': [
133 clihelp: 'Specify a valid matplotlib colormap for the heatmap. ' +
134 "Default: ${params.nanoplot_cm}",
135 cliflag: '-cm',
136 clivalue: (params.nanoplot_cm ?: '')
137 ],
138 'nanoplot_format': [
139 clihelp: 'Specify the output format of the plots, which are in addition to the html files. ' +
140 "Default: ${params.nanoplot_format}",
141 cliflag: '-f',
142 clivalue: (params.nanoplot_format ?: '')
143 ],
144 'nanoplot_plots': [
145 clihelp: 'Specify which bivariate plots have to be made [ kde, hex, dot ]. ' +
146 "Default: ${params.nanoplot_plots}",
147 cliflag: '--plots',
148 clivalue: (params.nanoplot_plots ?: '')
149 ],
150 'nanoplot_noN50': [
151 clihelp: 'Hide the N50 mark in the read length histogram. ' +
152 "Default: ${params.nanoplot_noN50}",
153 cliflag: '--no-N50',
154 clivalue: (params.nanoplot_noN50 ?: '')
155 ],
156 'nanoplot_N50': [
157 clihelp: 'Show the N50 mark in the read length histogram. ' +
158 "Default: ${params.nanoplot_N50}",
159 cliflag: '--N50',
160 clivalue: (params.nanoplot_N50 ?: '')
161 ],
162 'nanoplot_dpi': [
163 clihelp: 'Set the DPI for saving images. ' +
164 "Default: ${params.nanoplot_dpi}",
165 cliflag: '--dpi',
166 clivalue: (params.nanoplot_dpi ?: '')
167 ],
168 'nanoplot_hide_stats': [
169 clihelp: 'Do not add Pearson R stats in some bivariate plots. ' +
170 "Default: ${params.nanoplot_hide_stats}",
171 cliflag: '--hide_stats',
172 clivalue: (params.nanoplot_hide_stats ?: '')
173 ]
174 ]
175
176 toolspecs.each {
177 k, v -> tool.text['--' + k] = "${v.clihelp}"
178 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
179 }
180
181 return tool
182 }