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1 // Help text for seqkit rmdup within CPIPES.
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2
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3 def seqkitrmdupHelp(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_rmdup_run': [
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12 clihelp: 'Remove duplicate sequences using seqkit rmdup. Default: ' +
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13 (params.seqkit_rmdup_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_rmdup_n': [
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18 clihelp: 'Match and remove duplicate sequences by full name instead of just ID. ' +
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19 "Default: ${params.seqkit_rmdup_n}",
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20 cliflag: '-n',
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21 clivalue: (params.seqkit_rmdup_n ? ' ' : '')
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22 ],
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23 'seqkit_rmdup_s': [
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24 clihelp: 'Match and remove duplicate sequences by sequence content. ' +
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25 "Default: ${params.seqkit_rmdup_s}",
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26 cliflag: '-s',
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27 clivalue: (params.seqkit_rmdup_s ? ' ' : '')
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28 ],
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29 'seqkit_rmdup_d': [
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30 clihelp: 'Save the duplicated sequences to a file. ' +
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31 "Default: ${params.seqkit_rmdup_d}",
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32 cliflag: null,
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33 clivalue: null
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34 ],
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35 'seqkit_rmdup_D': [
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36 clihelp: 'Save the number and list of duplicated sequences to a file. ' +
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37 "Default: ${params.seqkit_rmdup_D}",
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38 cliflag: null,
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39 clivalue: null
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40 ],
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41 'seqkit_rmdup_i': [
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42 clihelp: 'Ignore case while using seqkit rmdup. ' +
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43 "Default: ${params.seqkit_rmdup_i}",
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44 cliflag: '-i',
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45 clivalue: (params.seqkit_rmdup_i ? ' ' : '')
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46 ],
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47 'seqkit_rmdup_P': [
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48 clihelp: "Only consider positive strand (i.e. 5') when comparing by sequence content. " +
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49 "Default: ${params.seqkit_rmdup_P}",
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50 cliflag: '-P',
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51 clivalue: (params.seqkit_rmdup_P ? ' ' : '')
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52 ]
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53 ]
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54
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55 toolspecs.each {
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56 k, v -> tool.text['--' + k] = "${v.clihelp}"
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57 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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58 }
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59
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60 return tool
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61 } |
