view snpsplit.xml @ 6:e711f63e99ff draft

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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>


**What it does**



SNPsplit prepares tab-delimited SNP files for TRAMS. It checks each line for entries that contain multiple consecutive bases and splits them over several lines.



- **Input**: tab delimited, format: Position Ref Pol
- Position is 1-based genomic coordinate

- Ref is the reference sequence

- Pol is the polymorphism 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 C*G*T AGG

=== ===== ===



**Output**:


=== = =

123 C A

125 T G

=== = =


  </help>

</tool>