<tool id="gencode_partition1" name="Gencode Partition">
  <description>an interval file</description>
  <command interpreter="python">split_by_partitions.py ${GALAXY_DATA_INDEX_DIR} $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command>
  <inputs>
    <param name="input1" type="data" format="interval" label="File to Partition"/>
  </inputs>
  <outputs>
    <data name="out_file1" format="bed"/>
  </outputs>
  <tests>
    <test>
      <param name="input1" value="encode_1.bed"/>
      <output name="out_file1" file="gencode_partition_out.bed"/>
    </test>
  </tests>
  <help>
For detailed information about partitioning, click here_.

.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups

Datasets are partitioned according to the protocol below:

A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories:
  1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
  2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
  3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
  4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
  5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
  6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
  7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.

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.. class:: infomark

**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. 

  </help>
</tool>