annotate phastCons.xml @ 12:2f4ea569f048

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<tool id="getScore" name="conservation">
  <description>phastCons or phyloP,vertebrate30way</description>
  <command interpreter="python">getGenomicScore.py $input $output $score_type $score_path $nbin $strand $outplot $span</command>
  <inputs>
      <param name="input" format="interval" type="data" label="Interval file"/>
      <param name="score_path" type="select" label="Select score" >
      <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm8/phastcons" >mm8-phastCons17way</option>
		  <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phastcon" selected="true">mm9-phastCons30way-vertebrate</option>
          <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phyloP30way">mm9-phyloP30way-vertebrate</option>
          <option value="/Users/xuebing/galaxy-dist/tool-data/genome/hg18/phastCons28wayPlacMam">hg18-phastCons28wayPlacMam</option>                      </param>
      <param name="score_type" type="select" label="Select score summary type" >
		  <option value="mean" selected="true">mean</option>
		  <option value="max">maximum</option>
		  <option value="min">minimum</option>
		  <option value="std">standard deviation</option>
		  <option value="coverage">coverage:fraction covered</option>
      </param>
      <param name="nbin" type="integer" value="1" label="number of bins"/> 
       <param name="span" size="10" type="float" value="0.1" label="loess span: smoothing parameter" help="value less then 0.1 disables smoothing"/>         
      <param name="strand" type="integer" value="0" label="Specify the strand column" help="leave 0 to ignore strand information. Only matters if using more than 1 bin"/>          
  </inputs>
  <outputs>
     <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
    <data format="interval" name="output" label="${tool.name} on ${on_string}[data]"/>
  </outputs>
  <help>

.. class:: infomark

The score for each interval is added as a new column appended at the end of the original file .

**Example**

If your original data has the following format:

+-----+-----+---+------+
|chrom|start|end|other2|
+-----+-----+---+------+

and you choose to return the mean of phastCons scores, your output will look like this:

+-----+-----+---+------+----+
|chrom|start|end|other2|mean|
+-----+-----+---+------+----+


</help>
</tool>