Mercurial > repos > test0004 > test0001
changeset 0:410a2d3c7b6c draft default tip
Uploaded
| author | test0004 |
|---|---|
| date | Thu, 30 Aug 2012 17:03:24 -0400 |
| parents | |
| children | |
| files | gencode_partition.xml |
| diffstat | 1 files changed, 45 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gencode_partition.xml Thu Aug 30 17:03:24 2012 -0400 @@ -0,0 +1,45 @@ +<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. + +----- + +.. class:: infomark + +**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + + </help> +</tool> \ No newline at end of file