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39 lines
2.0 KiB
XML
Executable File
39 lines
2.0 KiB
XML
Executable File
<tool id="gencode_partition1" name="Gencode Partition">
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<description>an interval file</description>
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<command interpreter="python">split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command>
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<inputs>
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<param name="input1" type="data" format="interval" label="File to Partition"/>
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</inputs>
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<outputs>
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<data name="out_file1" format="bed"/>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="encode_1.bed"/>
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<output name="out_file1" file="gencode_partition_out.bed"/>
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</test>
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</tests>
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<help>
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For detailed information about partitioning, click here_.
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.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups
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Datasets are partitioned according to the protocol below:
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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:
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1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
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2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
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3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
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4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
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5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
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6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
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7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
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-----
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.. class:: infomark
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**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
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</help>
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</tool> |