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annotate carpet-src-1/tools/CARPET/gff2bed_v2.xml @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="gff to bed wiggle" name="Gff2Wig" version="1.1.0">
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2 <description>easy UCSC visualization of your raw-data</description>
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3 <command interpreter="perl">gff2bed_v2.pl $input $col3 >$output</command>
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4 <inputs>
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5 <param format="gff" name="input" type="data" label="Source file"/>
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6 <param name="col3" size="20" type="text" value="Analysis" label="Analysis name"/>
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7 </inputs>
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8 <outputs>
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9 <data format="bed" name="output" file="wig-gff2bed.dat"/>
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10 </outputs>
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11
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12 <tests>
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13 <test>
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14 <param name="input" value="1.gff"/>
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15 <output name="output" file="wig-gff2bed.dat"/>
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16 </test>
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17 </tests>
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18 <help>
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19 .. class:: infomark
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20
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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21 **What it does**
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22
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23 This tool converts data from GFF format to WIGGLE format. This format allows the visuallization of raw intensity signals into the UCSC Genome Browser.
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24
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25 PLEASE, for more detailed information refer to the CARPET user Manual:
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26 click to download_ it.
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27
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28 .. _download: /static/example_file/CARPET_userManual.zip
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29
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30 --------
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31
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32 .. class:: infomark
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33
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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34 About formats
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35
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36 **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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37
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38 1. seqname - Must be a chromosome or scaffold.
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39 2. source - The program that generated this feature.
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40 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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41 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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42 5. end - The ending position of the feature (inclusive).
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43 6. score - A score or signal. If there is no score value, enter ".".
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44 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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45 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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46 9. group - All lines with the same group are linked together into a single item.
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47
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48 --------
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49
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50
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51 **Example**
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52
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53
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54 Nimblegen gives you back a GFF file with the coordinates of each probe and the normalized signal value --> log2(Cy5/Cy3) on the sixth column.
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56
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57 Click here_ to download a GFF file example.
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58
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59 .. _here: /static/example_file/GFF_file_norm.txt.zip
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60
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61 The following data in GFF format::
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62
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63 chr19 Nimblegen tiling_array 100000 1000051 -1.2 + . probe_name
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64 chr19 Nimblegen tiling_array 100100 1000151 2.9 + . probe_name
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65
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66 will be converted to WIG as shown below (Please note that a header will be added to the file)::
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67
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68 track type=wiggle_0 name="Analysis name" description="raw_data ratio" visibility=full autoscale=off maxHeightPixels=100:50:20 color=200,100,0 altColor=0,100,200
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69 chr19 1000000 1000050 -1.2
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70 chr19 1000100 1000150 2.9
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71
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72 .. class:: infomark
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73
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74 "Analysis name" will be shown in the UCSC Genome Browser as track name and can be defined by user.
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75
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76 Viusalize chip raw intensity:
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77
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78 .. image:: static/images/CARPET/ucsc2.jpg
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81
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82 </help>
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83 </tool>