<tool id="snv_annotate" name="SNV Annotator">
  <requirements>
    <requirement type="package">SNVMix</requirement>
  </requirements>
  <description>Annotates filtered SNVMix output that has been attached to codon information (outputs the same data with additional columns describing the predicted effect of the SNV)</description>
  <command interpreter="python">
    annotate.py
      -i $input_codon
      -o $output_anno
  </command>
 <inputs>
        <param name="input_codon" type="data" format="tabular" label="Select the codon-linked file to annotate" />
</inputs>

  <outputs>
    <data format="tabular" name="output_anno" label="${tool.name}: annotated SNV calls" />
  </outputs>
  <help>

**What it does**
Annotates filtered SNVMix output that has been attached to codon information (outputs the same data with additional columns describing the predicted effect of the SNV).
Requires input produced by the "SNP filtering and pre-annotation" tool

The additional columns are as follows:
1) Mutated form of the codon
2) Reference amino acid at that position
3) mutant amino acid at that position
4) CODING or SYNONYMOUS
5) Mutation with position and wild-type amino acid (separated by semicolon for genes with multiple transcripts)

Example input:
chr7:148139660 ENSG00000106462 -1 TAC 2 602;646; ENST00000350995;ENST00000320356; T A T:39,A:25,0.0000000000,1.0000000000,0.0000000000,2

Example output:
chr7:148139660 ENSG00000106462 -1 TAC 2 602;646; ENST00000350995;ENST00000320356; T A T:39,A:25,0.0000000000,1.0000000000,0.0000000000,2 TTC Y F CODING Y602F;Y646F

  </help>
</tool>