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comparison 1.0.0/lib/help/sourmashgather.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 sourmash gather within CPIPES.
2
3 def sourmashgatherHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'sourmashgather_run': [
12 clihelp: 'Run `sourmash gather` tool. Default: ' +
13 (params.sourmashgather_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'sourmashgather_n': [
18 clihelp: 'Number of results to report. ' +
19 'By default, will terminate at --sourmashgather_thr_bp value. ' +
20 "Default: ${params.sourmashgather_n}",
21 cliflag: '-n',
22 clivalue: (params.sourmashgather_n ?: '')
23 ],
24 'sourmashgather_thr_bp': [
25 clihelp: 'Reporting threshold (in bp) for estimated overlap with remaining query. ' +
26 "Default: ${params.sourmashgather_thr_bp}",
27 cliflag: '--threshold-bp',
28 clivalue: (params.sourmashgather_thr_bp ?: '')
29 ],
30 'sourmashgather_ignoreabn': [
31 clihelp: 'Do NOT use k-mer abundances if present. ' +
32 "Default: ${params.sourmashgather_ignoreabn}",
33 cliflag: '--ignore-abundance',
34 clivalue: (params.sourmashgather_ignoreabn ? ' ' : '')
35 ],
36 'sourmashgather_prefetch': [
37 clihelp: 'Use prefetch before gather. ' +
38 "Default: ${params.sourmashgather_prefetch}",
39 cliflag: '--prefetch',
40 clivalue: (params.sourmashgather_prefetch ? ' ' : '')
41 ],
42 'sourmashgather_noprefetch': [
43 clihelp: 'Do not use prefetch before gather. ' +
44 "Default: ${params.sourmashgather_noprefetch}",
45 cliflag: '--no-prefetch',
46 clivalue: (params.sourmashgather_noprefetch ? ' ' : '')
47 ],
48 'sourmashgather_ani_ci': [
49 clihelp: 'Output confidence intervals for ANI estimates. ' +
50 "Default: ${params.sourmashgather_ani_ci}",
51 cliflag: '--estimate-ani-ci',
52 clivalue: (params.sourmashgather_ani_ci ? ' ' : '')
53 ],
54 'sourmashgather_k': [
55 clihelp: 'The k-mer size to select. ' +
56 "Default: ${params.sourmashgather_k}",
57 cliflag: '-k',
58 clivalue: (params.sourmashgather_k ?: '')
59 ],
60 'sourmashgather_protein': [
61 clihelp: 'Choose a protein signature. ' +
62 "Default: ${params.sourmashgather_protein}",
63 cliflag: '--protein',
64 clivalue: (params.sourmashgather_protein ? ' ' : '')
65 ],
66 'sourmashgather_noprotein': [
67 clihelp: 'Do not choose a protein signature. ' +
68 "Default: ${params.sourmashgather_noprotein}",
69 cliflag: '--no-protein',
70 clivalue: (params.sourmashgather_noprotein ? ' ' : '')
71 ],
72 'sourmashgather_dayhoff': [
73 clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
74 "Default: ${params.sourmashgather_dayhoff}",
75 cliflag: '--dayhoff',
76 clivalue: (params.sourmashgather_dayhoff ? ' ' : '')
77 ],
78 'sourmashgather_nodayhoff': [
79 clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
80 "Default: ${params.sourmashgather_nodayhoff}",
81 cliflag: '--no-dayhoff',
82 clivalue: (params.sourmashgather_nodayhoff ? ' ' : '')
83 ],
84 'sourmashgather_hp': [
85 clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
86 "Default: ${params.sourmashgather_hp}",
87 cliflag: '--hp',
88 clivalue: (params.sourmashgather_hp ? ' ' : '')
89 ],
90 'sourmashgather_nohp': [
91 clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
92 "Default: ${params.sourmashgather_nohp}",
93 cliflag: '--no-hp',
94 clivalue: (params.sourmashgather_nohp ? ' ' : '')
95 ],
96 'sourmashgather_dna': [
97 clihelp: 'Choose DNA signature. ' +
98 "Default: ${params.sourmashgather_dna}",
99 cliflag: '--dna',
100 clivalue: (params.sourmashgather_dna ? ' ' : '')
101 ],
102 'sourmashgather_nodna': [
103 clihelp: 'Do not choose DNA signature. ' +
104 "Default: ${params.sourmashgather_nodna}",
105 cliflag: '--no-dna',
106 clivalue: (params.sourmashgather_nodna ? ' ' : '')
107 ],
108 'sourmashgather_scaled': [
109 clihelp: 'Scaled value should be between 100 and 1e6. ' +
110 "Default: ${params.sourmashgather_scaled}",
111 cliflag: '--scaled',
112 clivalue: (params.sourmashgather_scaled ?: '')
113 ],
114 'sourmashgather_inc_pat': [
115 clihelp: 'Search only signatures that match this pattern in name, filename, or md5. ' +
116 "Default: ${params.sourmashgather_inc_pat}",
117 cliflag: '--include-db-pattern',
118 clivalue: (params.sourmashgather_inc_pat ?: '')
119 ],
120 'sourmashgather_exc_pat': [
121 clihelp: 'Search only signatures that do not match this pattern in name, filename, or md5. ' +
122 "Default: ${params.sourmashgather_exc_pat}",
123 cliflag: '--exclude-db-pattern',
124 clivalue: (params.sourmashgather_exc_pat ?: '')
125 ]
126 ]
127
128 toolspecs.each {
129 k, v -> tool.text['--' + k] = "${v.clihelp}"
130 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
131 }
132
133 return tool
134 }