mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 05:45:37 +08:00
85 lines
3.8 KiB
XML
85 lines
3.8 KiB
XML
<tool id="gtf2bedgraph" name="GTF-to-BEDGraph" version="1.0.0">
|
|
<description>converter</description>
|
|
<edam_operations>
|
|
<edam_operation>operation_3434</edam_operation>
|
|
</edam_operations>
|
|
<command interpreter="python">gtf_to_bedgraph_converter.py $input $out_file1 $attribute_name</command>
|
|
<inputs>
|
|
<param format="gtf" name="input" type="data" label="Convert this query"/>
|
|
<param name="attribute_name" type="text" label="Attribute to Use for Value">
|
|
<validator type="empty_field" />
|
|
</param>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="bedgraph" name="out_file1" />
|
|
</outputs>
|
|
<tests>
|
|
<test>
|
|
<param name="input" value="gtf2bedgraph_in.gtf" ftype="gtf"/>
|
|
<param name="attribute_name" value="FPKM"/>
|
|
<output name="out_file1" file="gtf2bedgraph_out.bedgraph" ftype="bedgraph"/>
|
|
</test>
|
|
</tests>
|
|
<help>
|
|
|
|
**What it does**
|
|
|
|
This tool converts data from GTF format to BEDGraph format (scroll down for format description).
|
|
|
|
--------
|
|
|
|
**Example**
|
|
|
|
The following data in GFF format::
|
|
|
|
chr22 GeneA enhancer 10000000 10001000 500 + . gene_id "GeneA"; transcript_id "TranscriptAlpha"; FPKM "2.75"; frac "1.000000";
|
|
chr22 GeneA promoter 10010000 10010100 900 + . gene_id "GeneA"; transcript_id "TranscriptsAlpha"; FPKM "2.25"; frac "1.000000";
|
|
|
|
using the attribute name 'FPKM' will be converted to BEDGraph (**note** that 1 is subtracted from the start coordinate)::
|
|
|
|
|
|
chr22 9999999 10001000 2.75
|
|
chr22 10009999 10010100 2.25
|
|
|
|
------
|
|
|
|
.. class:: infomark
|
|
|
|
**About formats**
|
|
|
|
**GTF format** Gene Transfer Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GTF 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 - The group field is a list of attributes. Each attribute consists of a type/value pair. Attributes must end in a semi-colon, and be separated from any following attribute by exactly one space. The attribute list must begin with the two mandatory attributes: (i) gene_id value - A globally unique identifier for the genomic source of the sequence and (ii) transcript_id value - A globally unique identifier for the predicted transcript.
|
|
|
|
**BEDGraph format**
|
|
|
|
The bedGraph format is line-oriented. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track.
|
|
|
|
For the track definition line, all options are placed in a single line separated by spaces:
|
|
track type=bedGraph name=track_label description=center_label
|
|
visibility=display_mode color=r,g,b altColor=r,g,b
|
|
priority=priority autoScale=on|off alwaysZero=on|off
|
|
gridDefault=on|off maxHeightPixels=max:default:min
|
|
graphType=bar|points viewLimits=lower:upper
|
|
yLineMark=real-value yLineOnOff=on|off
|
|
windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16
|
|
|
|
The track type is REQUIRED, and must be bedGraph:
|
|
type=bedGraph
|
|
|
|
Following the track definition line are the track data in four column BED format::
|
|
|
|
chromA chromStartA chromEndA dataValueA
|
|
chromB chromStartB chromEndB dataValueB
|
|
|
|
</help>
|
|
</tool>
|