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annotate gff_to_bed.xml @ 10:c42c69aa81f8

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fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo
author vipints <vipin@cbio.mskcc.org>
date Thu, 23 Apr 2015 18:01:45 -0400
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1 <tool id="fml_gff2bed" name="GFF-to-BED" version="2.1.0">
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2 <description>converter</description>
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3 <command interpreter="python">gff_to_bed.py $inf_gff &gt; $bed_format
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4 </command>
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5 <inputs>
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6 <param format="gtf,gff,gff3" name="inf_gff" type="data" label="Convert this query" help="Provide genome annotation file in GFF, GTF, GFF3."/>
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7 </inputs>
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8 <outputs>
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9 <data format="bed" name="bed_format" label="${tool.name} on ${on_string}: Converted" />
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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="inf_gff" value="MB7_3R.gff3" />
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14 <output name="bed_format" file="MB7_3R.bed" />
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15 </test>
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16 </tests>
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17 <help>
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18
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19 **What it does**
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20
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21 This tool converts gene transcript annotation from GTF or GFF or GFF3 to UCSC wiggle 12 column BED format.
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22
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23 --------
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24
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25 **Example**
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26
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27 - The following data in GFF3::
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28
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29 ##gff-version 3
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30 chr1 protein_coding gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3
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31 chr1 protein_coding transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3
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32 chr1 protein_coding exon 11874 12227 0 + . Parent=uc001aaa.3
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33 chr1 protein_coding exon 12613 12721 0 + . Parent=uc001aaa.3
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34 chr1 protein_coding exon 13221 14409 0 + . Parent=uc001aaa.3
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35
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36 - Will be converted to UCSC Wiggle BED format::
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37
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38 chr1 11874 14409 uc001aaa.3 0 + 11874 14409 0 3 354,109,1189, 0,739,1347,
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39
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40 --------
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41
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42 **Reference**
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43
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44 **GFF-to-BED** is part of oqtans package and cited as [1]_.
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45
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46 .. [1] Sreedharan VT, Schultheiss SJ, Jean G et.al., Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics (2014). `10.1093/bioinformatics/btt731`_
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47
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48 .. _10.1093/bioinformatics/btt731: http://goo.gl/I75poH
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49
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50 --------
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51
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52 **About file formats**
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53
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54 **GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields::
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55
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56
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57 1. seqid - Must be a chromosome or scaffold or contig.
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58 2. source - The program that generated this feature.
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59 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
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60 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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61 5. stop - The ending position of the feature (inclusive).
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62 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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63 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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64 8. phase - 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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65 9. attributes - All lines with the same group are linked together into a single item.
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66
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67 **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
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68
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69 The first three BED fields (required) are::
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70
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71 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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72 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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73 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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74
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75 The additional BED fields (optional) are::
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76
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77 4. name - The name of the BED line.
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78 5. score - A score between 0 and 1000.
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79 6. strand - Defines the strand - either '+' or '-'.
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80 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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81 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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82 9. reserved - This should always be set to zero.
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83 10. blockCount - The number of blocks (exons) in the BED line.
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84 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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85 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
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86
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87 --------
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88
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89 **Copyright**
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90
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91 GFF-to-BED Wrapper Version 0.6 (Apr 2015)
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92
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93 2009-2015 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center
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94
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95 </help>
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96 </tool>