<?xml version="1.0"?>
<tool id="snpeff_to_peptides" name="SnpEff to Peptide fasta" version="0.0.1">
  <description> to create a Search DB fasta for variant SAP peptides</description>
  <command interpreter="python">snpeff_to_peptides.py  --input "$snpeff_vcf" --protein_fasta "$all_pep_fasta" --output "$peptide_variant_fasta"
  #if $leading_aa_num:
    --leading_aa_num $leading_aa_num
  #end if
  #if $trailing_aa_num:
    --trailing_aa_num $trailing_aa_num
  #end if
  </command>
  <inputs>
    <param name="snpeff_vcf" type="data" format="vcf" label="SnpEff generated VCF file with NON_SYNONYMOUS_CODING annotations"/> 
    <param name="all_pep_fasta" type="data" format="fasta,tabular" label="Ensembl all_pep.fa" 
           help="An Ensembl all_pep.fa file corresponding to the genome build used for SnpEff (May be converted to tabular fasta format)"/> 
    <param name="leading_aa_num" type="integer" value="30" min="0" optional="true" label="Preceeding AAs" 
           help="The number of Amino Acids to include before the variant position (leave blank to include all)"/>
    <param name="trailing_aa_num" type="integer" value="30" min="0" optional="true" label="Following AAs" 
           help="The number of Amino Acids to include after the variant position (leave blank to include all)"/>
  </inputs>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <outputs>
    <data name="peptide_variant_fasta" metadata_source="all_pep_fasta" format="fasta"/>
  </outputs>
  <tests>
    <test>
      <param name="snpeff_vcf" value="snpeff.vcf" ftype="vcf" dbkey="hg19"/>
      <param name="all_pep_fasta" value="all_pep.fa" ftype="fasta" dbkey="hg19"/>
      <param name="leading_aa_num" value="10"/>
      <param name="trailing_aa_num" value="10"/>
      <output name="peptide_variant_fasta" file="peptides_10_10.fa"/>
    </test>
    <test>
      <param name="snpeff_vcf" value="snpeff.vcf" ftype="vcf" dbkey="hg19"/>
      <param name="all_pep_fasta" value="all_pep.tabular" ftype="tabular" dbkey="hg19"/>
      <param name="leading_aa_num" value="10"/>
      <param name="trailing_aa_num" value="10"/>
      <output name="peptide_variant_fasta" file="peptides_10_10.fa"/>
    </test>
  </tests>
  <help>
**SnpEff to Peptide Fasta**

This generates a fasta file of peptide sequences with SAPs ( Single Amino acid Polymorphisms ) 
from the NON_SYNONYMOUS_CODING EFF annnotations from the SnpEff_ application.
The SnpEff VCF may be filtered or annotated using SnpSift.  

The following is appended to the fasta ID line:   snp_location:chr:position codon_change:nnn/nnn sap:AposA

For VCF entry::

  chr1    22846709        .       G       A       9.31    .       DP=2;VDB=0.0174;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V885M|1127|ZBTB40|protein_coding|CODING|ENST00000374651|12|1)  PL      40,6,0

The peptide fasta entry that matches transcript ID: ENST00000374651 would be::

  >ENSP00000363782 pep:known chromosome:GRCh37:1:22778472:22853855:1 gene:ENSG00000184677 transcript:ENST00000374651 gene_biotype:protein_coding transcript_biotype:protein_coding

The ID of the output peptide fasta ID would be::

  >ENSP00000363782 pep:sap chromosome:GRCh37:1:22778472:22853855:1 gene:ENSG00000184677 transcript:ENST00000374651 gene_biotype:protein_coding transcript_biotype:protein_coding snp_location:chr1:22846709 codon_change:Gtg/Atg sap:V885M


.. _SnpEff: http://snpeff.sourceforge.net/index.html

**Citation**

SnpEff citation:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]

SnpSift citation:
"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.

  </help>
</tool>