annotate maf_cpg_filter.xml @ 1:e5b0c8ca1399 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7

<tool id="cpgFilter" name="Mask CpG/non-CpG sites" version="1.0.0">
  <description> from MAF file</description>
  <requirements>
    <requirement type="package" version="0.7.1">bx-python</requirement>
  </requirements>
  <command interpreter="python">
  	maf_cpg_filter.py 
    $input 
    $out_file1 
    $masksite.type
    #if $masksite.type == "CpG":
     $masksite.definition
    #else:
     "NA"
   #end if
    -m $mask_char
  </command>
  <inputs>
    <page>
    	<param format="maf" name="input" type="data" label="Select data"/>
   		<param name="mask_char" type="select" label="Mask character">
    		<option value="0" selected="true">#</option>
          	<option value="1">$</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" 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" 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" />
      <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>