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Added tool version directory hierarchy for encode and extract tool directories.

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Greg Von Kuster
2008-02-22 14:18:41 +00:00
parent 1bb153a949
commit cabde35b99
24 changed files with 23 additions and 16 deletions
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tools/encode/gencode_partition.xml
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<tool id="gencode_partition1" name="Gencode Partition">
<description>an interval file</description>
<command interpreter="python2.4">split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 $input1_chromCol $input1_startCol $input1_endCol $input1_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.
-----
.. class:: infomark
**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
</help>
</tool>