kkonganti@11: // Help text for seqkit grep within CPIPES.
kkonganti@11: 
kkonganti@11: def seqkitgrepHelp(params) {
kkonganti@11: 
kkonganti@11:     Map tool = [:]
kkonganti@11:     Map toolspecs = [:]
kkonganti@11:     tool.text = [:]
kkonganti@11:     tool.helpparams = [:]
kkonganti@11: 
kkonganti@11:     toolspecs = [
kkonganti@11:         'seqkit_grep_n': [
kkonganti@11:             clihelp: 'Match by full name instead of just ID. ' +
kkonganti@11:                 "Default: " + (params.seqkit_grep_n ?: 'undefined'),
kkonganti@11:             cliflag: '--seqkit_grep_n',
kkonganti@11:             clivalue: (params.seqkit_grep_n ? ' ' : '')
kkonganti@11:         ], 
kkonganti@11:         'seqkit_grep_s': [
kkonganti@11:             clihelp: 'Search subseq on seq, both positive and negative ' +
kkonganti@11:                 'strand are searched, and mismatch allowed using flag --seqkit_grep_m. ' +
kkonganti@11:                 "Default: " + (params.seqkit_grep_s ?: 'undefined'),
kkonganti@11:             cliflag: '--seqkit_grep_s',
kkonganti@11:             clivalue: (params.seqkit_grep_s ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'seqkit_grep_c': [
kkonganti@11:             clihelp: 'Input is circular genome ' +
kkonganti@11:                 "Default: " + (params.seqkit_grep_c ?: 'undefined'),
kkonganti@11:             cliflag: '--seqkit_grep_c',
kkonganti@11:             clivalue: (params.seqkit_grep_c ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'seqkit_grep_C': [
kkonganti@11:             clihelp: 'Just print a count of matching records. With the ' +
kkonganti@11:                 '--seqkit_grep_v flag, count non-matching records. ' +
kkonganti@11:                 "Default: " + (params.seqkit_grep_v ?: 'undefined'),
kkonganti@11:             cliflag: '--seqkit_grep_v',
kkonganti@11:             clivalue: (params.seqkit_grep_v ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'seqkit_grep_i': [
kkonganti@11:             clihelp: 'Ignore case while using seqkit grep. ' +
kkonganti@11:                 "Default: " + (params.seqkit_grep_i ?: 'undefined'),
kkonganti@11:             cliflag: '--seqkit_grep_i',
kkonganti@11:             clivalue: (params.seqkit_grep_i ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'seqkit_grep_v': [
kkonganti@11:             clihelp: 'Invert the match i.e. select non-matching records. ' +
kkonganti@11:                 "Default: " + (params.seqkit_grep_v ?: 'undefined'),
kkonganti@11:             cliflag: '--seqkit_grep_v',
kkonganti@11:             clivalue: (params.seqkit_grep_v ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'seqkit_grep_m': [
kkonganti@11:             clihelp: 'Maximum mismatches when matching by sequence. ' +
kkonganti@11:                 "Default: " + (params.seqkit_grep_m ?: 'undefined'),
kkonganti@11:             cliflag: '--seqkit_grep_m',
kkonganti@11:             clivalue: (params.seqkit_grep_v ?: '')
kkonganti@11:         ],
kkonganti@11:         'seqkit_grep_r': [
kkonganti@11:             clihelp: 'Input patters are regular expressions. ' +
kkonganti@11:                 "Default: " + (params.seqkit_grep_m ?: 'undefined'),
kkonganti@11:             cliflag: '--seqkit_grep_m',
kkonganti@11:             clivalue: (params.seqkit_grep_v ?: '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }