Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/lib/help/centrifuge.nf @ 101:ce6d9548fe89
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:45:55 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 // Help text for centrifuge within CPIPES. |
| kkonganti@101 | 2 |
| kkonganti@101 | 3 def centrifugeHelp(params) { |
| kkonganti@101 | 4 |
| kkonganti@101 | 5 Map tool = [:] |
| kkonganti@101 | 6 Map toolspecs = [:] |
| kkonganti@101 | 7 tool.text = [:] |
| kkonganti@101 | 8 tool.helpparams = [:] |
| kkonganti@101 | 9 |
| kkonganti@101 | 10 toolspecs = [ |
| kkonganti@101 | 11 'centrifuge_x': [ |
| kkonganti@101 | 12 clihelp: "Absolute path to centrifuge database. Default: ${params.centrifuge_x}", |
| kkonganti@101 | 13 cliflag: '-x', |
| kkonganti@101 | 14 clivalue: null |
| kkonganti@101 | 15 ], |
| kkonganti@101 | 16 'centrifuge_save_unaligned': [ |
| kkonganti@101 | 17 clihelp: 'Save SINGLE-END reads that did not align. For PAIRED-END' + |
| kkonganti@101 | 18 " reads, save read pairs that did not align concordantly. Default: ${params.centrifuge_save_unaligned}", |
| kkonganti@101 | 19 cliflag: null, // Handled in modules logic. |
| kkonganti@101 | 20 clivalue: null |
| kkonganti@101 | 21 ], |
| kkonganti@101 | 22 'centrifuge_save_aligned': [ |
| kkonganti@101 | 23 clihelp: 'Save SINGLE-END reads that aligned. For PAIRED-END' + |
| kkonganti@101 | 24 " reads, save read pairs that aligned concordantly. Default: ${params.centrifuge_save_aligned}", |
| kkonganti@101 | 25 cliflag: null, // Handled in modules logic. |
| kkonganti@101 | 26 clivalue: null |
| kkonganti@101 | 27 ], |
| kkonganti@101 | 28 'centrifuge_out_fmt_sam': [ |
| kkonganti@101 | 29 clihelp: "Centrifuge output should be in SAM. Default: ${params.centrifuge_save_aligned}", |
| kkonganti@101 | 30 cliflag: null, // Handled in modules logic. |
| kkonganti@101 | 31 clivalue: null |
| kkonganti@101 | 32 ], |
| kkonganti@101 | 33 'centrifuge_extract_bug': [ |
| kkonganti@101 | 34 clihelp: "Extract this bug from centrifuge results." + |
| kkonganti@101 | 35 " Default: ${params.centrifuge_extract_bug}", |
| kkonganti@101 | 36 cliflag: null, // Handled in modules logic. |
| kkonganti@101 | 37 clivalue: null, |
| kkonganti@101 | 38 ], |
| kkonganti@101 | 39 'centrifuge_ignore_quals': [ |
| kkonganti@101 | 40 clihelp: 'Treat all quality values as 30 on Phred scale. ' + |
| kkonganti@101 | 41 "Default: ${params.centrifuge_ignore_quals}", |
| kkonganti@101 | 42 cliflag: '--ignore-quals', |
| kkonganti@101 | 43 clivalue: (params.centrifuge_ignore_quals ? ' ' : '') |
| kkonganti@101 | 44 ] |
| kkonganti@101 | 45 ] |
| kkonganti@101 | 46 |
| kkonganti@101 | 47 toolspecs.each { |
| kkonganti@101 | 48 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@101 | 49 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@101 | 50 } |
| kkonganti@101 | 51 |
| kkonganti@101 | 52 return tool |
| kkonganti@101 | 53 } |
| kkonganti@101 | 54 |