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