annotate galaxy-conf/GeneTrackToWig.xml @ 25:b43c420a6135 draft default tip

Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9

<tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.1.0">
  <description>converter</description>
  <command interpreter="bash">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command>
  <inputs>
      <param name="input" type="data" format="tabular" 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>
	<tests>
	  <test>
	    <param name="input" value="test.genetrack" ftype="tabular"/>
	    <param name="shift" value="73"/>
	    <param name="zero" value="true"/>
	    <param name="chromInfo" value="sacCer2"/>
	    <output name="output" file="geneTrackToWig1.wig"/>
    </test>
    <test>
	    <param name="input" value="test.genetrack" ftype="tabular"/>
	    <param name="shift" value="0"/>
	    <param name="zero" value="false"/>
	    <param name="chromInfo" value="sacCer2"/>
	    <output name="output" file="geneTrackToWig2.wig"/>
    </test>
  </tests>
<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>