view bigwig_to_wig.xml @ 5:4f227ae81c46 draft

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<tool id="bigwig_to_wig" name="BigWig to Wig" version="1.0.0">
  <description>converter</description>
  <command>/home/jens/bin/bigwig2wig_stdout -f $input -b $bin_size -l $mylab > $output 
  </command>
  <requirements>
    <requirement type="package">bigWigSummary</requirement>
    <requirement type="package">bigwig2wig</requirement>
    <requirement type="package">bigWigInfo</requirement>
  </requirements>
  <inputs>
    <param format="bigwig" name="input" type="data" label="BigWig file to convert">
    </param>
    <param name="bin_size" size="4" type="integer" value="500" label="Bin size" help="Must be an even integer > 100." />
    <param name="mylab" type="text" value="wiggle_file" label="Output file prefix" help="" />
  </inputs>
  <outputs>
    <data format="wig" name="output" label="${mylab}_density_bin${bin_size}.wig" />
  </outputs>
  <tests>
  </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>