Mercurial > repos > kkonganti > cfsan_cronology
comparison 0.2.0/lib/help/kmaindex.nf @ 11:a5f31c44f8c9
planemo upload
author | kkonganti |
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date | Mon, 15 Jul 2024 16:11:44 -0400 |
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10:ddf7a172bf30 | 11:a5f31c44f8c9 |
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1 // Help text for kma index within CPIPES. | |
2 | |
3 def kmaindexHelp(params) { | |
4 | |
5 Map tool = [:] | |
6 Map toolspecs = [:] | |
7 tool.text = [:] | |
8 tool.helpparams = [:] | |
9 | |
10 toolspecs = [ | |
11 'kmaindex_run': [ | |
12 clihelp: 'Run kma index tool. Default: ' + | |
13 (params.kmaindex_run ?: false), | |
14 cliflag: null, | |
15 clivalue: null | |
16 ], | |
17 'kmaindex_t_db': [ | |
18 clihelp: 'Add to existing DB. ' + | |
19 <<<<<<< HEAD | |
20 "Defaut: ${params.kmaindex_t_db}", | |
21 ======= | |
22 "Default: ${params.kmaindex_t_db}", | |
23 >>>>>>> 0.5.0 | |
24 cliflag: '-t_db', | |
25 clivalue: (params.kmaindex_t_db ? ' ' : '') | |
26 ], | |
27 'kmaindex_k': [ | |
28 clihelp: 'k-mer size. ' + | |
29 "Default: ${params.kmaindex_k}", | |
30 cliflag: '-k', | |
31 clivalue: (params.kmaindex_k ?: '') | |
32 ], | |
33 'kmaindex_m': [ | |
34 clihelp: 'Minimizer size. ' + | |
35 "Default: ${params.kmaindex_m}", | |
36 cliflag: '-m', | |
37 clivalue: (params.kmaindex_m ?: '') | |
38 ], | |
39 'kmaindex_hc': [ | |
40 clihelp: 'Homopolymer compression. ' + | |
41 "Default: ${params.kmaindex_hc}", | |
42 cliflag: '-hc', | |
43 clivalue: (params.kmaindex_hc ? ' ' : '') | |
44 ], | |
45 'kmaindex_ML': [ | |
46 clihelp: 'Minimum length of templates. Defaults to --kmaindex_k ' + | |
47 "Default: ${params.kmaindex_ML}", | |
48 cliflag: '-ML', | |
49 clivalue: (params.kmaindex_ML ?: '') | |
50 ], | |
51 'kmaindex_ME': [ | |
52 clihelp: 'Mega DB. ' + | |
53 "Default: ${params.kmaindex_ME}", | |
54 cliflag: '-ME', | |
55 clivalue: (params.kmaindex_ME ? ' ' : '') | |
56 ], | |
57 'kmaindex_Sparse': [ | |
58 clihelp: 'Make Sparse DB. ' + | |
59 "Default: ${params.kmaindex_Sparse}", | |
60 cliflag: '-Sparse', | |
61 clivalue: (params.kmaindex_Sparse ? ' ' : '') | |
62 ], | |
63 'kmaindex_ht': [ | |
64 clihelp: 'Homology template. ' + | |
65 "Default: ${params.kmaindex_ht}", | |
66 cliflag: '-ht', | |
67 clivalue: (params.kmaindex_ht ?: '') | |
68 ], | |
69 'kmaindex_hq': [ | |
70 clihelp: 'Homology query. ' + | |
71 "Default: ${params.kmaindex_hq}", | |
72 cliflag: '-hq', | |
73 clivalue: (params.kmaindex_hq ?: '') | |
74 ], | |
75 'kmaindex_and': [ | |
76 clihelp: 'Both homology thresholds have to reach. ' + | |
77 "Default: ${params.kmaindex_and}", | |
78 cliflag: '-and', | |
79 clivalue: (params.kmaindex_and ? ' ' : '') | |
80 ], | |
81 'kmaindex_nbp': [ | |
82 clihelp: 'No bias print. ' + | |
83 "Default: ${params.kmaindex_nbp}", | |
84 cliflag: '-nbp', | |
85 clivalue: (params.kmaindex_nbp ? ' ' : '') | |
86 ] | |
87 ] | |
88 | |
89 toolspecs.each { | |
90 k, v -> tool.text['--' + k] = "${v.clihelp}" | |
91 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] | |
92 } | |
93 | |
94 return tool | |
95 } |