root/galaxy-central/tools/regVariation/getIndels_2way.xml

<tool id="getIndels_2way" name="Fetch Indels">
  <description> from pairwise alignments</description>
  <command interpreter="python">
        getIndels.py $input1 $out_file1
  </command>
  <inputs>
    <page>
        <param format="maf" name="input1" type="data" label="Select data"/>
    </page>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" metadata_source="input1"/>
  </outputs>
  <requirements>
    <requirement type="python-module">numpy</requirement>
  </requirements>
  <tests>
    <test>
      <param name="input1" value="6.maf"/>
      <output name="out_file1" file="6_indels.tabular"/>
    </test>
  </tests>
 <help> 

.. class:: infomark

**What it does**

This tool estimates the number of indels for every alignment block of the MAF file. 

-----

.. class:: warningmark

**Note**

Any block/s not containing exactly 2 species will be omitted. 

-----

**Example**

- For the following alignment block::

   a score=7233.0
   s hg18.chr1     100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT
   s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC---- 

- running this tool will return::

   #Block   Source            Seq1_Start        Seq1_End  Seq2_Start    Seq2_End        Indel_length
   1       hg18.chr1            101              102         202             204              2
   1       rheMac2.chr11        103              104         204             205              1
   1       rheMac2.chr11        129              133         229             230              4
   
</help>  


</tool>