view bigwig_to_wig.xml @ 22:d7d071aa4927 draft

Uploaded

<tool id="bigwig_to_wig" name="BigWig to Wig" version="1.0.2">
    <description>converter</description>
    <command>bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output </command>
  <requirements>
      <requirement type="package">bigWigSummary</requirement>
      <requirement type="package">bigWigInfo</requirement>
  </requirements>
  <inputs>
      <param format="bigwig" name="input" type="data" label="BigWig file to convert" />
      <param name="bin_size" size="4" type="integer" value="500" label="Bin size" help="Must be an even integer > 100." />
      <param name="mylab" type="text" value="wiggle_file" label="Output file prefix" help="" />
  </inputs>
  <outputs>
      <data format="wig" name="output" label="${mylab}_density_bin${bin_size}.wig" />
  </outputs>
  <tests>
      <test>
	  <param name="input" value="1.bigwig" />
	  <param name="bin_size" value="500" />
	  <output name="output" file="1.wig" />	  
      <test>
  </tests>
  <help>

This tool converts a **BigWig** file to fixed step **Wiggle** format. 
Resolution is controlled through the bin size (the higher the size, the lower the resolution).

The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigInfo_ and bigWigSummary_.

.. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo
.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary

</help>
</tool>