/tools/liftover/standardize_wig.xml

<tool name="Standardize wig file" id="filter_std_wig">
  <description>Standardize a wig file to a given span</description>
  <command interpreter="command">/bin/bash $shscript</command>
  <inputs>
    <param ftype="wig" format="wig" name="wfile" type="data" label="WIGGLE file"/>
    <param name="span" type="select" label="Span">
        <option value="8">8</option>
        <option value="32">32</option>
        <option value="64">64</option>
        <option value="128">128</option>
    </param>
  </inputs>
  <outputs>
    <data format="wig" name="output" />
  </outputs>
  <configfiles>
    <configfile name="shscript">
#!/bin/bash

#set $dollar = chr(36)
#set $gt = chr(62)
#set $lt = chr(60)
#set $ad = chr(38)

standardize_wig.py $wfile $span $output ${ad}${gt}/dev/null
    
   </configfile>
  </configfiles>
<tests>
    <test maxseconds="3600" name="StandardizeWig_4">
    <param name="wfile" value="wiggle.wig" />
    <param name="span" value="128" />
    <output name="output" file="standardizewig_4/standardizewig_4.wig" />
  </test>
    <test maxseconds="3600" name="StandardizeWig_3">
    <param name="wfile" value="wiggle.wig" />
    <param name="span" value="64" />
    <output name="output" file="standardizewig_3/standardizewig_3.wig" />
  </test>
    <test maxseconds="3600" name="StandardizeWig_2">
    <param name="wfile" value="wiggle.wig" />
    <param name="span" value="32" />
    <output name="output" file="standardizewig_2/standardizewig_2.wig" />
  </test>
  <test maxseconds="3600" name="StandardizeWig_1">
    <param name="wfile" value="wiggle.wig" />
    <param name="span" value="8" />
    <output name="output" file="standardizewig_1/standardizewig_1.wig" />
  </test>
</tests>
  <help>
This tool converts a given wig file to conform to a given span. The
code is written by Jacqueline Wentz.

-----

**Parameters**

- **WIGGLE file** is selected from current history.
- **Span** is the final resolution in the converted WIGGLE file.

-----

**Output**

- **WIGGLE file** is the converted file.

  </help>

</tool>