<tool id="trams" name="TRAMS">

  <description>Tool for Rapid Annotation of Microbial SNPs</description>

  <command interpreter="python">trams.py $input1 $input2 $ref_format $annot $overl $sum</command>

  <inputs>

    <param name="input1" type="data" format="tabular" label="SNP table" />

    <param name="input2" type="data" format="txt" label="Reference genome" help="Reference genome file, should be genbank or embl file." />

    <param name="ref_format" type="select">

     <label>Reference file type</label>

      <option value="gb">Genbank</option>

      <option value="embl">EMBL</option>

    </param>

  </inputs>

  <outputs>

    <data name="annot" format="tabular" label="${tool.name} on ${on_string}: SNP annotation file" />

    <data name="overl" format="tabular" label="${tool.name} on ${on_string}: Overlap file" />

    <data name="sum" format="txt" label="${tool.name} on ${on_string}: Summary file" />

  </outputs>

  <help>



**What it does**



This tool annotates SNPs from a SNP table and a genbank or embl reference file.



**Input**



The SNP table has to be tabular (tab-delimited), with headers on the first line (strain names/numbers). Consecutive lines should contain SNP position in the first column, reference base in the second and SNP bases in consecutive columns. Any number of strains can be compared to the reference.



======== ==== ======= =======

Position Ref. Strain1 Strain2

102	 a    g       c

158      c    c       t

200      t    a       a

etc..    ..   ..      ..

======== ==== ======= =======




**Output**



TRAMS produces three output files. The **SNP annotation file** contains an annotation of each SNP in the input table, giving gene function and the type of SNP (synonymous, nonsynonymous, etc). The **Overlap file** reports on SNPs or ranges of SNPs that are located in multiple features (as defined in the reference genome file). These SNPs can be found in the annotation file once for each feature. The **Summary file** gives an overview of the number of SNPs in each strain and a breakdown of how the SNPs are spread over different types.

  </help>

</tool>
