/tools/filters/gtf2bedgraph.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 79 lines · 58 code · 21 blank · 0 comment · 0 complexity · cdb0998bfa73eb9de4ea8448e5c8fb28 MD5 · raw file
- <tool id="gtf2bedgraph" name="GTF-to-BEDGraph">
- <description>converter</description>
- <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"/>
- </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>