Mercurial > repos > xuebing > sharplabtool
comparison tools/encode/gencode_partition.xml @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:9071e359b9a3 |
|---|---|
| 1 <tool id="gencode_partition1" name="Gencode Partition"> | |
| 2 <description>an interval file</description> | |
| 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> | |
| 4 <inputs> | |
| 5 <param name="input1" type="data" format="interval" label="File to Partition"/> | |
| 6 </inputs> | |
| 7 <outputs> | |
| 8 <data name="out_file1" format="bed"/> | |
| 9 </outputs> | |
| 10 <tests> | |
| 11 <test> | |
| 12 <param name="input1" value="encode_1.bed"/> | |
| 13 <output name="out_file1" file="gencode_partition_out.bed"/> | |
| 14 </test> | |
| 15 </tests> | |
| 16 <help> | |
| 17 For detailed information about partitioning, click here_. | |
| 18 | |
| 19 .. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups | |
| 20 | |
| 21 Datasets are partitioned according to the protocol below: | |
| 22 | |
| 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: | |
| 24 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) | |
| 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) | |
| 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) | |
| 27 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. | |
| 28 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. | |
| 29 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. | |
| 30 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. | |
| 31 | |
| 32 ----- | |
| 33 | |
| 34 .. class:: infomark | |
| 35 | |
| 36 **Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. | |
| 37 | |
| 38 </help> | |
| 39 </tool> |