annotate galaxy-conf/GeneTrackToWig.xml @ 12:81d5b81fb3c2 draft

Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.

<tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.0.0">
  <description>converter</description>
  <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command>
  <inputs>
      <param name="input" type="data" format="genetrack" label="Input GeneTrack index" />
      <param name="shift" type="integer" value="0" optional="true" label="Shift +/- strand counts by this amount when merging" />
  	  <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" />
  </inputs>
  <outputs>
      <data name="output" format="wig" metadata_source="input" />
  </outputs>
	
<help>
  
This tool will convert GeneTrack_ format files into Wig files, optionally offsetting the + and - strand counts by a specified value before merging them.

.. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html

.. class:: warningmark
	
This tool requires GeneTrack formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.

</help>
</tool>