root/galaxy-central/tools/encode/gencode_partition.xml

リビジョン 2, 2.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

  • 属性 svn:executable の設定値 *
行番号 
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>
17For 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
21Datasets are partitioned according to the protocol below:
22
23A 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>
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