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1 // Help text for centrifuge within CPIPES.
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2
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3 def centrifugeHelp(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 'centrifuge_x': [
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12 clihelp: "Absolute path to centrifuge database. Default: ${params.centrifuge_x}",
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13 cliflag: '-x',
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14 clivalue: null
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15 ],
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16 'centrifuge_save_unaligned': [
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17 clihelp: 'Save SINGLE-END reads that did not align. For PAIRED-END' +
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18 " reads, save read pairs that did not align concordantly. Default: ${params.centrifuge_save_unaligned}",
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19 cliflag: null, // Handled in modules logic.
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20 clivalue: null
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21 ],
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22 'centrifuge_save_aligned': [
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23 clihelp: 'Save SINGLE-END reads that aligned. For PAIRED-END' +
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24 " reads, save read pairs that aligned concordantly. Default: ${params.centrifuge_save_aligned}",
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25 cliflag: null, // Handled in modules logic.
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26 clivalue: null
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27 ],
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28 'centrifuge_out_fmt_sam': [
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29 clihelp: "Centrifuge output should be in SAM. Default: ${params.centrifuge_save_aligned}",
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30 cliflag: null, // Handled in modules logic.
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31 clivalue: null
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32 ],
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33 'centrifuge_extract_bug': [
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34 clihelp: "Extract this bug from centrifuge results." +
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35 " Default: ${params.centrifuge_extract_bug}",
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36 cliflag: null, // Handled in modules logic.
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37 clivalue: null,
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38 ],
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39 'centrifuge_ignore_quals': [
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40 clihelp: 'Treat all quality values as 30 on Phred scale. ' +
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41 "Default: ${params.centrifuge_ignore_quals}",
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42 cliflag: '--ignore-quals',
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43 clivalue: (params.centrifuge_ignore_quals ? ' ' : '')
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44 ]
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45 ]
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46
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47 toolspecs.each {
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48 k, v -> tool.text['--' + k] = "${v.clihelp}"
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49 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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50 }
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51
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52 return tool
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53 }
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54
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