Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.2/lib/help/seqkitrmdup.nf @ 130:04f6ac8ca13c
planemo upload
| author | kkonganti |
|---|---|
| date | Wed, 03 Jul 2024 15:16:39 -0400 |
| parents | 52045ea4679d |
| children |
| rev | line source |
|---|---|
| kkonganti@105 | 1 // Help text for seqkit rmdup within CPIPES. |
| kkonganti@105 | 2 |
| kkonganti@105 | 3 def seqkitrmdupHelp(params) { |
| kkonganti@105 | 4 |
| kkonganti@105 | 5 Map tool = [:] |
| kkonganti@105 | 6 Map toolspecs = [:] |
| kkonganti@105 | 7 tool.text = [:] |
| kkonganti@105 | 8 tool.helpparams = [:] |
| kkonganti@105 | 9 |
| kkonganti@105 | 10 toolspecs = [ |
| kkonganti@105 | 11 'seqkit_rmdup_run': [ |
| kkonganti@105 | 12 clihelp: 'Remove duplicate sequences using seqkit rmdup. Default: ' + |
| kkonganti@105 | 13 (params.seqkit_rmdup_run ?: false), |
| kkonganti@105 | 14 cliflag: null, |
| kkonganti@105 | 15 clivalue: null |
| kkonganti@105 | 16 ], |
| kkonganti@105 | 17 'seqkit_rmdup_n': [ |
| kkonganti@105 | 18 clihelp: 'Match and remove duplicate sequences by full name instead of just ID. ' + |
| kkonganti@105 | 19 "Defaut: ${params.seqkit_rmdup_n}", |
| kkonganti@105 | 20 cliflag: '-n', |
| kkonganti@105 | 21 clivalue: (params.seqkit_rmdup_n ? ' ' : '') |
| kkonganti@105 | 22 ], |
| kkonganti@105 | 23 'seqkit_rmdup_s': [ |
| kkonganti@105 | 24 clihelp: 'Match and remove duplicate sequences by sequence content. ' + |
| kkonganti@105 | 25 "Defaut: ${params.seqkit_rmdup_s}", |
| kkonganti@105 | 26 cliflag: '-s', |
| kkonganti@105 | 27 clivalue: (params.seqkit_rmdup_s ? ' ' : '') |
| kkonganti@105 | 28 ], |
| kkonganti@105 | 29 'seqkit_rmdup_d': [ |
| kkonganti@105 | 30 clihelp: 'Save the duplicated sequences to a file. ' + |
| kkonganti@105 | 31 "Defaut: ${params.seqkit_rmdup_d}", |
| kkonganti@105 | 32 cliflag: null, |
| kkonganti@105 | 33 clivalue: null |
| kkonganti@105 | 34 ], |
| kkonganti@105 | 35 'seqkit_rmdup_D': [ |
| kkonganti@105 | 36 clihelp: 'Save the number and list of duplicated sequences to a file. ' + |
| kkonganti@105 | 37 "Defaut: ${params.seqkit_rmdup_D}", |
| kkonganti@105 | 38 cliflag: null, |
| kkonganti@105 | 39 clivalue: null |
| kkonganti@105 | 40 ], |
| kkonganti@105 | 41 'seqkit_rmdup_i': [ |
| kkonganti@105 | 42 clihelp: 'Ignore case while using seqkit rmdup. ' + |
| kkonganti@105 | 43 "Defaut: ${params.seqkit_rmdup_i}", |
| kkonganti@105 | 44 cliflag: '-i', |
| kkonganti@105 | 45 clivalue: (params.seqkit_rmdup_i ? ' ' : '') |
| kkonganti@105 | 46 ], |
| kkonganti@105 | 47 'seqkit_rmdup_P': [ |
| kkonganti@105 | 48 clihelp: "Only consider positive strand (i.e. 5') when comparing by sequence content. " + |
| kkonganti@105 | 49 "Defaut: ${params.seqkit_rmdup_P}", |
| kkonganti@105 | 50 cliflag: '-P', |
| kkonganti@105 | 51 clivalue: (params.seqkit_rmdup_P ? ' ' : '') |
| kkonganti@105 | 52 ] |
| kkonganti@105 | 53 ] |
| kkonganti@105 | 54 |
| kkonganti@105 | 55 toolspecs.each { |
| kkonganti@105 | 56 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@105 | 57 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@105 | 58 } |
| kkonganti@105 | 59 |
| kkonganti@105 | 60 return tool |
| kkonganti@105 | 61 } |