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/tools/filters/gtf2bedgraph.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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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
22This tool converts data from GTF format to BEDGraph format (scroll down for format description).
23
24--------
25
26**Example**
27
28The 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
33using 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
59The 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
61For 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
70The track type is REQUIRED, and must be bedGraph:
71  type=bedGraph
72
73Following 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>