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1 // Help text for sourmash_filter_hits.py (sfhpy) within CPIPES.
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2 def sfhpyHelp(params) {
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3
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4 Map tool = [:]
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5 Map toolspecs = [:]
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6 tool.text = [:]
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7 tool.helpparams = [:]
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8
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9 toolspecs = [
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10 'sfhpy_run': [
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11 clihelp: 'Run the sourmash_filter_hits.py ' +
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12 'script. Default: ' +
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13 (params.sfhpy_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 'sfhpy_fcn': [
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18 clihelp: 'Column name by which filtering of rows should be applied. ' +
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19 "Default: ${params.sfhpy_fcn}",
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20 cliflag: '-fcn',
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21 clivalue: (params.sfhpy_fcn ?: '')
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22 ],
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23 'sfhpy_fcv': [
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24 clihelp: 'Remove genomes whose match with the query FASTQ is less than ' +
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25 'this much. ' +
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26 "Default: ${params.sfhpy_fcv}",
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27 cliflag: '-fcv',
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28 clivalue: (params.sfhpy_fcv ?: '')
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29 ],
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30 'sfhpy_gt': [
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31 clihelp: 'Apply greather than or equal to condition on numeric values of ' +
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32 '--sfhpy_fcn column. ' +
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33 "Default: ${params.sfhpy_gt}",
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34 cliflag: '-gt',
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35 clivalue: (params.sfhpy_gt ? ' ' : '')
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36 ],
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37 'sfhpy_lt': [
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38 clihelp: 'Apply less than or equal to condition on numeric values of ' +
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39 '--sfhpy_fcn column. ' +
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40 "Default: ${params.sfhpy_lt}",
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41 cliflag: '-gt',
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42 clivalue: (params.sfhpy_lt ? ' ' : '')
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43 ],
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44 'sfhpy_all': [
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45 clihelp: 'Instead of just the column value, print entire row. ' +
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46 "Default: ${params.sfhpy_all}",
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47 cliflag: '-all',
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48 clivalue: (params.sfhpy_all ? ' ' : '')
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49 ],
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50 ]
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51
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52 toolspecs.each {
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53 k, v -> tool.text['--' + k] = "${v.clihelp}"
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54 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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55 }
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56
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57 return tool
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58 } |
