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1 // Help text for seqkit `grep` within CPIPES.
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2
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3 def seqkitgrepHelp(params) {
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4
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5 Map tool = [:]
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6 Map toolspecs = [:]
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7 tool.text = [:]
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8 tool.helpparams = [:]
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9
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10 toolspecs = [
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11 'seqkit_grep_run': [
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12 clihelp: 'Run the seqkit `grep` tool. Default: ' +
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13 (params.seqkit_grep_run ?: false),
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14 cliflag: null,
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15 clivalue: null
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16 ],
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17 'seqkit_grep_n': [
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18 clihelp: 'Match by full name instead of just ID. ' +
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19 "Default: " + (params.seqkit_grep_n ?: 'undefined'),
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20 cliflag: '--seqkit_grep_n',
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21 clivalue: (params.seqkit_grep_n ? ' ' : '')
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22 ],
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23 'seqkit_grep_s': [
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24 clihelp: 'Search subseq on seq, both positive and negative ' +
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25 'strand are searched, and mismatch allowed using flag --seqkit_grep_m. ' +
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26 "Default: " + (params.seqkit_grep_s ?: 'undefined'),
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27 cliflag: '--seqkit_grep_s',
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28 clivalue: (params.seqkit_grep_s ? ' ' : '')
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29 ],
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30 'seqkit_grep_c': [
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31 clihelp: 'Input is circular genome ' +
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32 "Default: " + (params.seqkit_grep_c ?: 'undefined'),
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33 cliflag: '--seqkit_grep_c',
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34 clivalue: (params.seqkit_grep_c ? ' ' : '')
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35 ],
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36 'seqkit_grep_C': [
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37 clihelp: 'Just print a count of matching records. With the ' +
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38 '--seqkit_grep_v flag, count non-matching records. ' +
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39 "Default: " + (params.seqkit_grep_v ?: 'undefined'),
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40 cliflag: '--seqkit_grep_v',
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41 clivalue: (params.seqkit_grep_v ? ' ' : '')
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42 ],
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43 'seqkit_grep_i': [
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44 clihelp: 'Ignore case while using seqkit grep. ' +
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45 "Default: " + (params.seqkit_grep_i ?: 'undefined'),
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46 cliflag: '--seqkit_grep_i',
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47 clivalue: (params.seqkit_grep_i ? ' ' : '')
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48 ],
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49 'seqkit_grep_v': [
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50 clihelp: 'Invert the match i.e. select non-matching records. ' +
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51 "Default: " + (params.seqkit_grep_v ?: 'undefined'),
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52 cliflag: '--seqkit_grep_v',
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53 clivalue: (params.seqkit_grep_v ? ' ' : '')
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54 ],
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55 'seqkit_grep_m': [
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56 clihelp: 'Maximum mismatches when matching by sequence. ' +
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57 "Default: " + (params.seqkit_grep_m ?: 'undefined'),
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58 cliflag: '--seqkit_grep_m',
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59 clivalue: (params.seqkit_grep_v ?: '')
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60 ],
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61 'seqkit_grep_r': [
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62 clihelp: 'Input patters are regular expressions. ' +
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63 "Default: " + (params.seqkit_grep_m ?: 'undefined'),
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64 cliflag: '--seqkit_grep_m',
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65 clivalue: (params.seqkit_grep_v ?: '')
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66 ]
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67 ]
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68
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69 toolspecs.each {
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70 k, v -> tool.text['--' + k] = "${v.clihelp}"
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71 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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72 }
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73
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74 return tool
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75 } |
