[2] | 1 | <tool id="gencode_partition1" name="Gencode Partition">
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| 2 | <description>an interval file</description>
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| 3 | <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>
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| 4 | <inputs>
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| 5 | <param name="input1" type="data" format="interval" label="File to Partition"/>
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| 6 | </inputs>
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| 7 | <outputs>
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| 8 | <data name="out_file1" format="bed"/>
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| 9 | </outputs>
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| 10 | <tests>
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| 11 | <test>
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| 12 | <param name="input1" value="encode_1.bed"/>
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| 13 | <output name="out_file1" file="gencode_partition_out.bed"/>
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| 14 | </test>
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| 15 | </tests>
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| 16 | <help>
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| 17 | For detailed information about partitioning, click here_.
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| 18 |
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| 19 | .. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups
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| 20 |
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| 21 | Datasets are partitioned according to the protocol below:
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| 22 |
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| 23 | 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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| 24 | 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
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| 25 | 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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| 26 | 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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| 27 | 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
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| 28 | 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
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| 29 | 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
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| 30 | 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
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| 31 |
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| 32 | -----
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| 33 |
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| 34 | .. class:: infomark
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| 35 |
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| 36 | **Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
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| 37 |
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| 38 | </help>
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| 39 | </tool> |
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