Mercurial > repos > vipints > fml_gff3togtf
annotate fml_gff_converter_programs/galaxy/bed_to_gff3.xml @ 0:ed53dca1c6ff
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | vipints |
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date | Tue, 07 Jun 2011 17:26:20 -0400 |
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1 <tool id="fml_bed2gff" name="BED_to_GFF3" version="1.0.0"> |
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2 <description>converter</description> |
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3 <command interpreter="python">bed_to_gff3_converter.py $inf_bed > $gff_format |
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4 </command> |
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5 <inputs> |
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6 <param format="bed" name="inf_bed" type="data" label="Convert this query" help="Please look at About format section."/> |
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7 </inputs> |
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8 <outputs> |
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9 <data format="gff3" name="gff_format" /> |
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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_bed" value="ccds_genes.bed" /> |
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14 <output name="gff_format" file="ccds_genes.gff3" /> |
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15 </test> |
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16 <test> |
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17 <param name="inf_bed" value="hs_2009.bed" /> |
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18 <output name="gff_format" file="hs_2009.gff3" /> |
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19 </test> |
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20 </tests> |
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21 <help> |
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22 |
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23 **What it does** |
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24 |
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25 This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format. |
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26 |
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27 -------- |
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28 |
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29 **Example** |
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30 |
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31 - The following data in UCSC Wiggle BED format:: |
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32 |
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33 chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347, |
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34 |
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35 - Will be converted to GFF3 format:: |
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36 |
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37 ##gff-version 3 |
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38 chr1 bed2gff gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3 |
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39 chr1 bed2gff transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3 |
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40 chr1 bed2gff exon 11874 12227 0 + . Parent=uc001aaa.3 |
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41 chr1 bed2gff exon 12613 12721 0 + . Parent=uc001aaa.3 |
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42 chr1 bed2gff exon 13221 14409 0 + . Parent=uc001aaa.3 |
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43 |
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44 -------- |
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45 |
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46 **About formats** |
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47 |
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48 **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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49 |
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50 The first three BED fields (required) are:: |
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51 |
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52 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). |
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53 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) |
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54 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). |
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55 |
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56 The additional BED fields (optional) are:: |
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57 |
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58 4. name - The name of the BED line. |
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59 5. score - A score between 0 and 1000. |
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60 6. strand - Defines the strand - either '+' or '-'. |
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61 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. |
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62 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. |
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63 9. reserved - This should always be set to zero. |
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64 10. blockCount - The number of blocks (exons) in the BED line. |
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65 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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66 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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67 |
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68 **GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields: |
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69 |
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70 1. seqid - Must be a chromosome or scaffold or contig. |
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71 2. source - The program that generated this feature. |
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72 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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73 4. start - The starting position of the feature in the sequence. The first base is numbered 1. |
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74 5. stop - The ending position of the feature (inclusive). |
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75 6. score - A score between 0 and 1000. If there is no score value, enter ".". |
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76 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). |
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77 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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78 9. attributes - All lines with the same group are linked together into a single item. |
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79 |
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80 -------- |
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81 |
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82 This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de) |
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83 </help> |
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84 </tool> |