<tool id="substitutions1" name="Fetch substitutions " version="1.0.0">
  <description> from pairwise alignments</description>
  <command interpreter="python">
  	substitutions.py 
  	$input 
  	$out_file1
  </command>
  <inputs>
    <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" metadata_source="input"/>
  </outputs>

  <tests>
    <test>
      <param name="input" value="Interval2Maf_pairwise_out.maf"/>
      <output name="out_file1" file="subs.out"/>
    </test>
  </tests>
 <help> 

.. class:: infomark

**What it does**

This tool takes a pairwise MAF file as input and fetches substitutions per alignment block.

-----

.. class:: warningmark

**Note**

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

  </help>  
</tool>