20
+ − 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>