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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> |