https://github.com/galaxyproject/galaxy
Tip revision: 9cdfd18f5027fdd0fec87a0982771c87d6a5640e authored by Dannon on 05 August 2020, 14:05:28 UTC
Merge pull request #10069 from natefoo/semicolon-uwsgi-pass
Merge pull request #10069 from natefoo/semicolon-uwsgi-pass
Tip revision: 9cdfd18
gff2bed.xml
<tool id="gff2bed1" name="GFF-to-BED" version="1.0.1">
<description>converter</description>
<edam_operations>
<edam_operation>operation_3434</edam_operation>
</edam_operations>
<command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
<inputs>
<param format="gff" name="input" type="data" label="Convert this dataset"/>
</inputs>
<outputs>
<data format="bed" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input" value="5.gff" ftype="gff"/>
<output name="out_file1" file="gff2bed_out.bed"/>
</test>
<test>
<param name="input" value="gff2bed_in2.gff" ftype="gff"/>
<output name="out_file1" file="gff2bed_out2.bed"/>
</test>
<test>
<!-- Test conversion of gff3 file. -->
<param name="input" value="5.gff3" ftype="gff"/>
<output name="out_file1" file="gff2bed_out3.bed"/>
</test>
</tests>
<help>
**What it does**
This tool converts data from GFF format to BED format (scroll down for format description).
--------
**Example**
The following data in GFF format::
chr22 GeneA enhancer 10000000 10001000 500 + . TGA
chr22 GeneA promoter 10010000 10010100 900 + . TGA
Will be converted to BED (**note** that 1 is subtracted from the start coordinate)::
chr22 9999999 10001000 enhancer 0 +
chr22 10009999 10010100 promoter 0 +
------
.. class:: infomark
**About formats**
**BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
The first three BED fields (required) are::
1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
The additional BED fields (optional) are::
4. name - The name of the BED line.
5. score - A score between 0 and 1000.
6. strand - Defines the strand - either '+' or '-'.
7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
9. reserved - This should always be set to zero.
10. blockCount - The number of blocks (exons) in the BED line.
11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
13. expCount - The number of experiments.
14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.
**GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields::
1. seqname - Must be a chromosome or scaffold.
2. source - The program that generated this feature.
3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. end - The ending position of the feature (inclusive).
6. score - A score between 0 and 1000. If there is no score value, enter ".".
7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
9. group - All lines with the same group are linked together into a single item.
</help>
</tool>