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1 // Help text for medaka `stitch` within CPIPES.
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2
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3 def medakastitchHelp(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 'medakastitch_min_depth': [
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12 clihelp: 'Sites with depth lower than this will not be polished. ' +
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13 "Default: ${params.medakastitch_min_depth}",
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14 cliflag: '--min_depth',
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15 clivalue: (params.medakastitch_min_depth ?: '')
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16 ],
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17 'medakastitch_no_fillgaps': [
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18 clihelp: "Don't fill gaps in consensus sequence with draft sequence. " +
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19 "Default: ${params.medakastitch_no_fillgaps}",
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20 cliflag: '--no-fillgaps',
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21 clivalue: (params.medakastitch_no_fillgaps ? ' ' : '')
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22 ],
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23 'medakastitch_fill_char': [
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24 clihelp: 'Use a designated character to fill gaps. ' +
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25 "Default: ${params.medakastitch_fill_char}",
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26 cliflag: '--fill_char',
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27 clivalue: (params.medakastitch_fill_char ?: '')
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28 ],
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29 'medakastitch_regions': [
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30 clihelp: 'Genomic regions to analyze, or a bed file. ' +
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31 "Default: ${params.medakastitch_regions}",
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32 cliflag: '--regions',
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33 clivalue: (params.medakastitch_regions ?: '')
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34 ],
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35 'medakastitch_quals': [
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36 clihelp: 'Output with per-base quality scores (fastq). ' +
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37 "Default: ${params.medakastitch_quals}",
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38 cliflag: '--qualities',
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39 clivalue: (params.medakastitch_quals ? ' ' : '')
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40 ]
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41 ]
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42
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43 toolspecs.each {
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44 k, v -> tool.text['--' + k] = "${v.clihelp}"
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45 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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46 }
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47
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48 return tool
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49 } |
