Mercurial > repos > xuebing > sharplabtool
comparison phastCons.xml @ 11:b7f1d9f8f3bc
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| author | xuebing |
|---|---|
| date | Sat, 10 Mar 2012 07:59:27 -0500 |
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| 10:1558594a3c2e | 11:b7f1d9f8f3bc |
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| 1 <tool id="getScore" name="conservation"> | |
| 2 <description>phastCons or phyloP,vertebrate30way</description> | |
| 3 <command interpreter="python">getGenomicScore.py $input $output $score_type $score_path $nbin $strand $outplot $span</command> | |
| 4 <inputs> | |
| 5 <param name="input" format="interval" type="data" label="Interval file"/> | |
| 6 <param name="score_path" type="select" label="Select score" > | |
| 7 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm8/phastcons" >mm8-phastCons17way</option> | |
| 8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phastcon" selected="true">mm9-phastCons30way-vertebrate</option> | |
| 9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phyloP30way">mm9-phyloP30way-vertebrate</option> | |
| 10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/hg18/phastCons28wayPlacMam">hg18-phastCons28wayPlacMam</option> </param> | |
| 11 <param name="score_type" type="select" label="Select score summary type" > | |
| 12 <option value="mean" selected="true">mean</option> | |
| 13 <option value="max">maximum</option> | |
| 14 <option value="min">minimum</option> | |
| 15 <option value="std">standard deviation</option> | |
| 16 <option value="coverage">coverage:fraction covered</option> | |
| 17 </param> | |
| 18 <param name="nbin" type="integer" value="1" label="number of bins"/> | |
| 19 <param name="span" size="10" type="float" value="0.1" label="loess span: smoothing parameter" help="value less then 0.1 disables smoothing"/> | |
| 20 <param name="strand" type="integer" value="0" label="Specify the strand column" help="leave 0 to ignore strand information. Only matters if using more than 1 bin"/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/> | |
| 24 <data format="interval" name="output" label="${tool.name} on ${on_string}[data]"/> | |
| 25 </outputs> | |
| 26 <help> | |
| 27 | |
| 28 .. class:: infomark | |
| 29 | |
| 30 The score for each interval is added as a new column appended at the end of the original file . | |
| 31 | |
| 32 **Example** | |
| 33 | |
| 34 If your original data has the following format: | |
| 35 | |
| 36 +-----+-----+---+------+ | |
| 37 |chrom|start|end|other2| | |
| 38 +-----+-----+---+------+ | |
| 39 | |
| 40 and you choose to return the mean of phastCons scores, your output will look like this: | |
| 41 | |
| 42 +-----+-----+---+------+----+ | |
| 43 |chrom|start|end|other2|mean| | |
| 44 +-----+-----+---+------+----+ | |
| 45 | |
| 46 | |
| 47 </help> | |
| 48 </tool> |