<?xml version="1.0"?>

<tool id="hgvs_annotation_2" name="Annotate an HGVS table">
  <requirements>
    <requirement type="package">genesplicer</requirement>
	    <requirement type="package">human</requirement>
		    <requirement type="package">score3.pl</requirement>
			    <requirement type="package">score5.pl</requirement>
  </requirements>

  <description>with deleterious AA and splicing change predictions, protein domain disruptions, etc.</description>
  <version_string>hgvs_table_annotate -v</version_string>
  <command interpreter="perl">hgvs_table_annotate $__tool_data_path__ -q /sift/hg19 /polyphen2/hg19.txt.gz /dbs/gerp/hg19 /dbs/TissueDistributionDBs/human.v2009-07-30.tab /dbs/pathways/KEGG.human.2012-09-25.txt /dbs/interpro_supermatch_hg19.bed /dbs/OMIM/morbidmap $input_hgvs_table $out_hgvs_annotated_table /hg19.fa</command>
  <inputs>
    <param format="achri_snp_table" name="input_hgvs_table" type="data" label="Variant calls table with HGVS syntax"/>
  </inputs>
  <outputs>
    <data format="achri_annotated_snp_table" name="out_hgvs_annotated_table" type="data" label="Functionally annotated HGVS variant table"/>
  </outputs>

  <tests>
  </tests>

  <help>
This tool reports several functional attributes, and potential for functional disturbance, based on genes that have declared sequence variants. 
These results can be used to help find the genetic cause of a clinical phenotype.
  </help>

</tool>