root/galaxy-central/tools/regVariation/maf_cpg_filter.xml

<tool id="cpgFilter" name="Mask CpG/non-CpG sites" version="1.0.0">
  <description> from MAF file</description>
  <command interpreter="python">
        maf_cpg_filter.py 
    $input 
    $out_file1 
    $masksite.type
    #if $masksite.type == "CpG":
     $masksite.definition
    #else:
     "NA"
   #end if
    -m $mask_char
  </command>
  <inputs>
    <page>
        <param format="maf" name="input" type="data" label="Select data"/>
                <param name="mask_char" size="5" type="select" label="Mask character">
                <option value="0" selected="true">#</option>
                <option value="1">$</option>
                <option value="2">^</option>
                <option value="3">*</option>
                <option value="4">?</option>
                <option value="5">N</option>
        </param>
        <conditional name="masksite">
            <param name="type" size="5" type="select" label="Sites to be masked">
                <option value="CpG" selected="true">CpG sites</option>
                <option value="nonCpG">non-CpG sites</option>
             </param>
            <when value="CpG">
                <param name="definition" size="5" type="select" label="Definition">
                    <option value="0" selected="true">Inclusive</option>
                    <option value="1">Restricted</option>
                 </param>
            </when>
            <when value="nonCpG" />
        </conditional>
    </page>
  </inputs>
  <outputs>
    <data format="maf" name="out_file1" metadata_source="input"/>
  </outputs>
  <requirements>
    <requirement type="python-module">numpy</requirement>
  </requirements>
  <tests>
    <test>
      <param name="input" value="6.maf"/>
      <param name="mask_char" value="0"/>
      <param name="type" value="CpG" />
      <param name="definition" value="0" />
      <output name="out_file1" file="6_mask_cpg.maf"/>
    </test>
    <test>
      <param name="input" value="6.maf"/>
      <param name="mask_char" value="0"/>
      <param name="type" value="nonCpG" />
      <param name="definition" value="NA" />
      <output name="out_file1" file="6_mask_noncpg.maf"/>
    </test>
  </tests>
 <help> 

.. class:: infomark

**What it does**

This tool takes a MAF file as input and masks CpG sites in every alignment block of the MAF file. 

-----

.. class:: warningmark

**Note**

*Inclusive definition* defines CpG sites as those sites that are CG in at least one of the species.

*Restricted definition* considers sites to be CpG if they are CG in at least one of the species, however, sites that are part of overlapping CpGs are excluded.

For more information on CpG site definitions, please refer this article_.

.. _article: http://mbe.oxfordjournals.org/cgi/content/full/23/3/565

  </help>  


</tool>