Mercurial > repos > xuebing > sharplabtool
comparison tools/filters/gtf2bedgraph.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="gtf2bedgraph" name="GTF-to-BEDGraph"> | |
| 2 <description>converter</description> | |
| 3 <command interpreter="python">gtf_to_bedgraph_converter.py $input $out_file1 $attribute_name</command> | |
| 4 <inputs> | |
| 5 <param format="gtf" name="input" type="data" label="Convert this query"/> | |
| 6 <param name="attribute_name" type="text" label="Attribute to Use for Value"/> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data format="bedgraph" name="out_file1" /> | |
| 10 </outputs> | |
| 11 <tests> | |
| 12 <test> | |
| 13 <param name="input" value="gtf2bedgraph_in.gtf" ftype="gtf"/> | |
| 14 <param name="attribute_name" value="FPKM"/> | |
| 15 <output name="out_file1" file="gtf2bedgraph_out.bedgraph" ftype="bedgraph"/> | |
| 16 </test> | |
| 17 </tests> | |
| 18 <help> | |
| 19 | |
| 20 **What it does** | |
| 21 | |
| 22 This tool converts data from GTF format to BEDGraph format (scroll down for format description). | |
| 23 | |
| 24 -------- | |
| 25 | |
| 26 **Example** | |
| 27 | |
| 28 The following data in GFF format:: | |
| 29 | |
| 30 chr22 GeneA enhancer 10000000 10001000 500 + . gene_id "GeneA"; transcript_id "TranscriptAlpha"; FPKM "2.75"; frac "1.000000"; | |
| 31 chr22 GeneA promoter 10010000 10010100 900 + . gene_id "GeneA"; transcript_id "TranscriptsAlpha"; FPKM "2.25"; frac "1.000000"; | |
| 32 | |
| 33 using the attribute name 'FPKM' will be converted to BEDGraph (**note** that 1 is subtracted from the start coordinate):: | |
| 34 | |
| 35 | |
| 36 chr22 9999999 10001000 2.75 | |
| 37 chr22 10009999 10010100 2.25 | |
| 38 | |
| 39 ------ | |
| 40 | |
| 41 .. class:: infomark | |
| 42 | |
| 43 **About formats** | |
| 44 | |
| 45 **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:: | |
| 46 | |
| 47 1. seqname - Must be a chromosome or scaffold. | |
| 48 2. source - The program that generated this feature. | |
| 49 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon". | |
| 50 4. start - The starting position of the feature in the sequence. The first base is numbered 1. | |
| 51 5. end - The ending position of the feature (inclusive). | |
| 52 6. score - A score between 0 and 1000. If there is no score value, enter ".". | |
| 53 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). | |
| 54 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 '.'. | |
| 55 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. | |
| 56 | |
| 57 **BEDGraph format** | |
| 58 | |
| 59 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. | |
| 60 | |
| 61 For the track definition line, all options are placed in a single line separated by spaces: | |
| 62 track type=bedGraph name=track_label description=center_label | |
| 63 visibility=display_mode color=r,g,b altColor=r,g,b | |
| 64 priority=priority autoScale=on|off alwaysZero=on|off | |
| 65 gridDefault=on|off maxHeightPixels=max:default:min | |
| 66 graphType=bar|points viewLimits=lower:upper | |
| 67 yLineMark=real-value yLineOnOff=on|off | |
| 68 windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16 | |
| 69 | |
| 70 The track type is REQUIRED, and must be bedGraph: | |
| 71 type=bedGraph | |
| 72 | |
| 73 Following the track definition line are the track data in four column BED format:: | |
| 74 | |
| 75 chromA chromStartA chromEndA dataValueA | |
| 76 chromB chromStartB chromEndB dataValueB | |
| 77 | |
| 78 </help> | |
| 79 </tool> |