<?xml version="1.0" encoding="UTF-8"?>
<?eclipse version="3.0"?>

<plugin> 
  <extension point="org.knime.workbench.repository.categories"> 
    <category description="/community/NgsToolbox/Read Mapping" icon="icons/category.png" path="/community/NgsToolbox" name="Read Mapping" level-id="Read Mapping"/>
    <category description="/community/NgsToolbox" icon="icons/category.png" path="/community" name="NgsToolbox" level-id="NgsToolbox"/>
    <category description="/community/NgsToolbox/SNP Calling" icon="icons/category.png" path="/community/NgsToolbox" name="SNP Calling" level-id="SNP Calling"/>
    <category description="/community/NgsToolbox/SAM and BAM Manipulation" icon="icons/category.png" path="/community/NgsToolbox" name="SAM and BAM Manipulation" level-id="SAM and BAM Manipulation"/>
    <category description="/community/NgsToolbox/VCF and BCF" icon="icons/category.png" path="/community/NgsToolbox" name="VCF and BCF" level-id="VCF and BCF"/>
  </extension>  
  <extension point="org.knime.workbench.repository.nodes"> 
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BowtieAlignerSE.BowtieAlignerSENodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BowtieAlignerSE.BowtieAlignerSENodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BwaBwaswSE.BwaBwaswSENodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BwaBwaswSE.BwaBwaswSENodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.SamtoolsMPileup.SamtoolsMPileupNodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.SamtoolsMPileup.SamtoolsMPileupNodeFactory" category-path="/community/NgsToolbox/SNP Calling"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BamToSam.BamToSamNodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BamToSam.BamToSamNodeFactory" category-path="/community/NgsToolbox/SAM and BAM Manipulation"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BwaBwaswPE.BwaBwaswPENodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BwaBwaswPE.BwaBwaswPENodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.Bowtie2Indexer.Bowtie2IndexerNodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.Bowtie2Indexer.Bowtie2IndexerNodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BwaSamSE.BwaSamSENodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BwaSamSE.BwaSamSENodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.Bowtie2AlignerSE.Bowtie2AlignerSENodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.Bowtie2AlignerSE.Bowtie2AlignerSENodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.SamToBam.SamToBamNodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.SamToBam.SamToBamNodeFactory" category-path="/community/NgsToolbox/SAM and BAM Manipulation"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.SortBam.SortBamNodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.SortBam.SortBamNodeFactory" category-path="/community/NgsToolbox/SAM and BAM Manipulation"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BcfToVcf.BcfToVcfNodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BcfToVcf.BcfToVcfNodeFactory" category-path="/community/NgsToolbox/VCF and BCF"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BwaSamPE.BwaSamPENodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BwaSamPE.BwaSamPENodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BowtieAlignerPE.BowtieAlignerPENodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BowtieAlignerPE.BowtieAlignerPENodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BowtieIndexer.BowtieIndexerNodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BowtieIndexer.BowtieIndexerNodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.Bowtie2AlignerPE.Bowtie2AlignerPENodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.Bowtie2AlignerPE.Bowtie2AlignerPENodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
    <node factory-class="de.seqan.ngs_toolbox.knime.nodes.BwaIndexer.BwaIndexerNodeFactory" id="de.seqan.ngs_toolbox.knime.nodes.BwaIndexer.BwaIndexerNodeFactory" category-path="/community/NgsToolbox/Read Mapping"/>
  </extension>  
  <extension point="org.knime.product.splashExtension"> 
    <splashExtension icon="icons/splash.png" id="de.seqan.ngs_toolbox.icons.splashIcon"/>
  </extension>  
  <extension point="org.knime.base.filehandling.mimetypes"> 
    <mimetype name="application/x-fasta">
      <fileextension name="fa"/>
      <fileextension name="fasta"/>
    </mimetype>
    <mimetype name="application/x-fastq">
      <fileextension name="fq"/>
      <fileextension name="fastq"/>
    </mimetype>
    <mimetype name="application/x-sam">
      <fileextension name="sam"/>
    </mimetype>
    <mimetype name="application/x-bam">
      <fileextension name="bam"/>
    </mimetype>
    <mimetype name="application/x-bowtie-index">
      <fileextension name="ebwt"/>
    </mimetype>
    <mimetype name="application/x-bowtie2-index">
      <fileextension name="bt2"/>
    </mimetype>
    <mimetype name="application/x-bcf">
      <fileextension name="bcf"/>
    </mimetype>
    <mimetype name="application/x-vcf">
      <fileextension name="vcf"/>
    </mimetype>
    <mimetype name="application/x-bwa-index">
      <fileextension name="bwaidx"/>
    </mimetype>
  </extension> 
</plugin>
