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comparison 0.2.0/lib/help/pirate.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 pirate within CPIPES.
2
3 def pirateHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'pirate_run': [
12 clihelp: 'Run pirate tool. Default: ' +
13 (params.pirate_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'pirate_steps': [
18 clihelp: '% identity thresholds to use for pangenome construction. ' +
19 "Default: ${params.pirate_steps}",
20 cliflag: '-s',
21 clivalue: (params.pirate_steps ?: '')
22 ],
23 'pirate_features': [
24 clihelp: 'Choose features to use for pangenome construction. ' +
25 'Multiple may be entered, seperated by a comma' +
26 "Default: ${params.pirate_features}",
27 cliflag: '-f',
28 clivalue: (params.pirate_features ?: '')
29 ],
30 'pirate_nucl': [
31 clihelp: 'CDS are not translated to AA sequence. ' +
32 "Default: ${params.pirate_nucl}",
33 cliflag: '-n',
34 clivalue: (params.pirate_nucl ? ' ' : '')
35 ],
36 'pirate_pan_opt': [
37 clihelp: 'Additional arguments to pass to pangenome_contruction. ' +
38 "Default: ${params.pirate_pan_opt}",
39 cliflag: '--pan-opt',
40 clivalue: (params.pirate_pan_opt ?: '')
41 ],
42 'pirate_pan_off': [
43 clihelp: "Don't run pangenome tool. " +
44 "Default: ${params.pirate_pan_off}",
45 cliflag: '--pan-off',
46 clivalue: (params.pirate_pan_off ? ' ' : '')
47 ],
48 'pirate_min_len': [
49 clihelp: 'Minimum length for feature extraction. ' +
50 "Default: ${params.pirate_min_len}",
51 cliflag: '--min-len',
52 clivalue: (params.pirate_min_len ?: '')
53 ],
54 'pirate_para_off': [
55 clihelp: 'Switch off paralog identification. ' +
56 "Default: ${params.pirate_para_off}",
57 cliflag: '--para-off',
58 clivalue: (params.pirate_para_off ?: '')
59 ],
60 'pirate_para_args': [
61 clihelp: 'Options to pass to paralog splitting algorithm. ' +
62 "Default: ${params.pirate_para_args}",
63 cliflag: '--para-args',
64 clivalue: (params.pirate_para_args ?: '')
65 ],
66 'pirate_classify_off': [
67 clihelp: 'Do not classify paralogs, assumes this has been ' +
68 'run previously. ' +
69 "Default: ${params.pirate_classify_off}",
70 cliflag: '--classify-off',
71 clivalue: (params.pirate_classify_off ? ' ' : '')
72 ],
73 'pirate_align': [
74 clihelp: 'align all genes and produce core/pangenome alignments. ' +
75 "Default: ${params.pirate_align}",
76 cliflag: '--align',
77 clivalue: (params.pirate_align ? ' ' : '')
78 ],
79 'pirate_rplots': [
80 clihelp: 'Plot summaries using R. ' +
81 "Default: ${params.pirate_rplots}",
82 cliflag: '--rplots',
83 clivalue: (params.pirate_rplots ? ' ' : '')
84 ]
85 ]
86
87 toolspecs.each {
88 k, v -> tool.text['--' + k] = "${v.clihelp}"
89 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
90 }
91
92 return tool
93 }