<opt
  name="fbbulk-hetr3"
  relid="h3b2"
  make_current="1"
  >

  <!-- see site_defaults for more included configs -->
<include>site_defaults</include>

<title>DHGP/FlyBase Heterochromatin rel 3.2</title>
  
<doc name="Release.txt"><![CDATA[
  D. melanogaster heterochomatin genome data from 
  Drosophila Heterochromatin Genome Project, www.dhgp.org
  Release  ${rel}, dated ${date}.
  
  See release notes at <a href="${release_url}">${release_url}</a>
 ]]></doc>
  
  <include>fbreleases</include>
  
  <!-- 
  From: cdsmith <cdsmith@fruitfly.org>
  Date: Mon, 10 Jan 2005 12:30:09 -0800
  I have updated XML for you for Release 3.2b ..
  Release3.2b_01102005 
  heterchrom/chado_dmel_h_r3_2b.gz for pg dump
  -->

  <org>dmel</org>
  <species>Drosophila_melanogaster</species>
  <golden_path>'chromosome_arm'</golden_path>
  <seq_ontology>SO</seq_ontology>

  <!-- dang; blank here becomes {} in xmlsimple -->
  <analysis_where_clause> -- none  </analysis_where_clause>
  <est_where_clause> -- none  </est_where_clause>
  <GFF_source>DHGP</GFF_source>


  <!-- override default fff config; 
  dang xmlsimple/config2 cant handle joining included config + override here array entry
  -->
  <fileset_override
    id="fff"
    path="fff/.+\.fff"
    input="feature_table"
    title="FFF Genome features"
    config="dmelhetfeatconv"
    handler="FeatureWriter"
    dogzip="0"
    />
  <fileset_override id="dummy" title="placeholder for xmlsimple"/>


    <!-- need to put in ENV for subsequent chadofeatsql.xml config -->
  <featdump
    path="tmp/featdump/\w+.tsv"
    config="chadofeatsql"
    tag="feature_sql"
    type="feature_table"
    splitname="chadofeat"
    >
    
    <target>chromosomes</target>
    <target>features</target>
    <target>analysis</target>
  </featdump>

 
  <!-- use to add parent ids to features .. change tag parentidpattern ? -->
  <idpattern>(FBgn|FBti)\d+</idpattern>

  <!-- feature sets to make fasta bulk files -->
  <featset>gene</featset>
  <featset>transcript</featset>
  <featset>CDS</featset>  <!-- dna of protein coding sequence -->
  <featset>translation</featset> <!-- protein aminos -->
  <featset>ncRNA</featset> <!-- combines tRNA, miscRNA -->
  <featset>transposon</featset>
  <featset>gene_extended2000</featset>
  <featset>pseudogene</featset>
  <featset>intergenic</featset>
  <featset>chromosome</featset>

  <!-- feature sets to make blast indices -->
  <blastset>gene</blastset>
  <blastset>transcript</blastset>
  <blastset>translation</blastset>
  <blastset>ncRNA</blastset>
  <blastset>intergenic</blastset>
  <blastset>chromosome</blastset>


</opt>
