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<?xml version="1.0"?>

<tool id="hgvs_group_alt_variants" name="Group alternate transcript effects">
  <description>to reduce the number of rows in a HGVS table</description>
  <version_string>hgvs_collapse_transcripts -v</version_string>
  <command interpreter="perl">hgvs_collapse_transcripts $input_hgvs_annotated_table $out_hgvs_annotated_table</command>
  <inputs>
    <param format="achri_annotated_snp_table" name="input_hgvs_annotated_table" type="data" label="Annotated variant calls table with HGVS syntax, one line per alternate transcript"/>
  </inputs>
  <outputs>
    <data format="achri_annotated_snp_table" name="out_hgvs_annotated_table" type="data" label="Variant table with one row for all transcripts wih same AA mod"/>
  </outputs>

  <tests>
  </tests>

  <help>
  This tool collapses multiple rows in an HGVS annotated variant table if they refer to the same genomic variant, and the amino acid HGVS syntax is the same except for the residue number.
  The row with the lowest numeric suffix for the model transcript (e.g. NM_000245 is before NM1002345) will have its cDNA and AA positions reported, and the alternate IDs are appoended to the transcript ID field separated by ';'.
  </help>

</tool>