<tool id="indels_3way" name="Fetch Indels"  version="1.0.3">
  <description> from 3-way alignments</description>
  <command interpreter="perl">
  	parseMAF_smallIndels.pl $input1 $out_file1 $outgroup
  </command>
  <inputs>
    <page>
    	<param format="maf" name="input1" type="data" label="Select data"/>
    	<param name="outgroup" type="select" label="Select outgroup species">
          <options>
            <filter type="data_meta" ref="input1" key="species" />
          </options>  
      	</param>
    </page>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" metadata_source="input1"/>
    <!--<data format="tabular" name="out_file2" metadata_source="input1"/>-->
  </outputs>
  <tests>
    <test>
      <param name="input1" value="3way.maf"/>
      <param name="outgroup" value="canFam2"/>
      <output name="out_file1" file="indels_3way.tabular"/>
    </test>
  </tests>
 <help> 

.. class:: infomark

**What it does**

This tool consists of the first module from the computational pipeline to identify indels as described in Kvikstad et al., 2007. Note that the generated output does not include subsequent filtering steps.

Deletions in a particular species are identified as one or more consecutive gap columns within an alignment block, given that the orthologous positions in the other two species contain nucleotides of
equal length. 
Similarly, insertions in a particular species are identified as one or more consecutive nucleotide columns within an alignment block, given that the orthologous positions in the other two
species contain gaps.

*Kvikstad E. M. et al. (2007). A Macaques-Eye View of Human Insertions and Deletions: Differences in Mechanisms. PLoS Computational Biology 3(9):e176*

-----

.. class:: warningmark

**Note**

Any block/s not containing exactly 3 sequences will be omitted. 

  </help>  


</tool>