Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.6.1/lib/help/seqkitrmdup.nf @ 15:1972677994a6
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 07 Sep 2023 10:27:12 -0400 |
| parents | 749faef1caa9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 // Help text for seqkit rmdup within CPIPES. |
| kkonganti@11 | 2 |
| kkonganti@11 | 3 def seqkitrmdupHelp(params) { |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 Map tool = [:] |
| kkonganti@11 | 6 Map toolspecs = [:] |
| kkonganti@11 | 7 tool.text = [:] |
| kkonganti@11 | 8 tool.helpparams = [:] |
| kkonganti@11 | 9 |
| kkonganti@11 | 10 toolspecs = [ |
| kkonganti@11 | 11 'seqkit_rmdup_run': [ |
| kkonganti@11 | 12 clihelp: 'Remove duplicate sequences using seqkit rmdup. Default: ' + |
| kkonganti@11 | 13 (params.seqkit_rmdup_run ?: false), |
| kkonganti@11 | 14 cliflag: null, |
| kkonganti@11 | 15 clivalue: null |
| kkonganti@11 | 16 ], |
| kkonganti@11 | 17 'seqkit_rmdup_n': [ |
| kkonganti@11 | 18 clihelp: 'Match and remove duplicate sequences by full name instead of just ID. ' + |
| kkonganti@11 | 19 "Default: ${params.seqkit_rmdup_n}", |
| kkonganti@11 | 20 cliflag: '-n', |
| kkonganti@11 | 21 clivalue: (params.seqkit_rmdup_n ? ' ' : '') |
| kkonganti@11 | 22 ], |
| kkonganti@11 | 23 'seqkit_rmdup_s': [ |
| kkonganti@11 | 24 clihelp: 'Match and remove duplicate sequences by sequence content. ' + |
| kkonganti@11 | 25 "Default: ${params.seqkit_rmdup_s}", |
| kkonganti@11 | 26 cliflag: '-s', |
| kkonganti@11 | 27 clivalue: (params.seqkit_rmdup_s ? ' ' : '') |
| kkonganti@11 | 28 ], |
| kkonganti@11 | 29 'seqkit_rmdup_d': [ |
| kkonganti@11 | 30 clihelp: 'Save the duplicated sequences to a file. ' + |
| kkonganti@11 | 31 "Default: ${params.seqkit_rmdup_d}", |
| kkonganti@11 | 32 cliflag: null, |
| kkonganti@11 | 33 clivalue: null |
| kkonganti@11 | 34 ], |
| kkonganti@11 | 35 'seqkit_rmdup_D': [ |
| kkonganti@11 | 36 clihelp: 'Save the number and list of duplicated sequences to a file. ' + |
| kkonganti@11 | 37 "Default: ${params.seqkit_rmdup_D}", |
| kkonganti@11 | 38 cliflag: null, |
| kkonganti@11 | 39 clivalue: null |
| kkonganti@11 | 40 ], |
| kkonganti@11 | 41 'seqkit_rmdup_i': [ |
| kkonganti@11 | 42 clihelp: 'Ignore case while using seqkit rmdup. ' + |
| kkonganti@11 | 43 "Default: ${params.seqkit_rmdup_i}", |
| kkonganti@11 | 44 cliflag: '-i', |
| kkonganti@11 | 45 clivalue: (params.seqkit_rmdup_i ? ' ' : '') |
| kkonganti@11 | 46 ], |
| kkonganti@11 | 47 'seqkit_rmdup_P': [ |
| kkonganti@11 | 48 clihelp: "Only consider positive strand (i.e. 5') when comparing by sequence content. " + |
| kkonganti@11 | 49 "Default: ${params.seqkit_rmdup_P}", |
| kkonganti@11 | 50 cliflag: '-P', |
| kkonganti@11 | 51 clivalue: (params.seqkit_rmdup_P ? ' ' : '') |
| kkonganti@11 | 52 ] |
| kkonganti@11 | 53 ] |
| kkonganti@11 | 54 |
| kkonganti@11 | 55 toolspecs.each { |
| kkonganti@11 | 56 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@11 | 57 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@11 | 58 } |
| kkonganti@11 | 59 |
| kkonganti@11 | 60 return tool |
| kkonganti@11 | 61 } |