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<tool id="snpsplit" name="SNP splitter">
  <description>splits multicharacter entries into separate lines</description>
  <command interpreter="python">snpsplit.py $input $output</command>
  <inputs>
    <param name="input" type="data" format="tabular" label="SNP table" />
  </inputs>
  <outputs>
    <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
  </outputs>
  <help>

Input: tab delimited, format Position Ref Mut
Position is 1-based genomic coordinate
Ref is the reference sequence
Mut is the mutant sequence

Ref en Mut sequences consisting of more than one character will be split up into separate lines. Example:
Input:  
123 CGT ATG
Output: 
123 C A
124 G T
125 T G

Bases that are the same in both columns, will be skipped. Example:
Input:  
123 CGT AGG
Output: 
123 C A
125 T G

  </help>
</tool>