Mercurial > repos > matces > carpet_toolsuite
comparison carpet-src-1/tools/CARPET/gff2bed_v2.xml @ 0:cdd489d98766
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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| -1:000000000000 | 0:cdd489d98766 |
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| 1 <tool id="gff to bed wiggle" name="Gff2Wig" version="1.1.0"> | |
| 2 <description>easy UCSC visualization of your raw-data</description> | |
| 3 <command interpreter="perl">gff2bed_v2.pl $input $col3 >$output</command> | |
| 4 <inputs> | |
| 5 <param format="gff" name="input" type="data" label="Source file"/> | |
| 6 <param name="col3" size="20" type="text" value="Analysis" label="Analysis name"/> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data format="bed" name="output" file="wig-gff2bed.dat"/> | |
| 10 </outputs> | |
| 11 | |
| 12 <tests> | |
| 13 <test> | |
| 14 <param name="input" value="1.gff"/> | |
| 15 <output name="output" file="wig-gff2bed.dat"/> | |
| 16 </test> | |
| 17 </tests> | |
| 18 <help> | |
| 19 .. class:: infomark | |
| 20 | |
| 21 **What it does** | |
| 22 | |
| 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. | |
| 24 | |
| 25 PLEASE, for more detailed information refer to the CARPET user Manual: | |
| 26 click to download_ it. | |
| 27 | |
| 28 .. _download: /static/example_file/CARPET_userManual.zip | |
| 29 | |
| 30 -------- | |
| 31 | |
| 32 .. class:: infomark | |
| 33 | |
| 34 About formats | |
| 35 | |
| 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: | |
| 37 | |
| 38 1. seqname - Must be a chromosome or scaffold. | |
| 39 2. source - The program that generated this feature. | |
| 40 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon". | |
| 41 4. start - The starting position of the feature in the sequence. The first base is numbered 1. | |
| 42 5. end - The ending position of the feature (inclusive). | |
| 43 6. score - A score or signal. If there is no score value, enter ".". | |
| 44 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). | |
| 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 '.'. | |
| 46 9. group - All lines with the same group are linked together into a single item. | |
| 47 | |
| 48 -------- | |
| 49 | |
| 50 | |
| 51 **Example** | |
| 52 | |
| 53 | |
| 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. | |
| 55 | |
| 56 | |
| 57 Click here_ to download a GFF file example. | |
| 58 | |
| 59 .. _here: /static/example_file/GFF_file_norm.txt.zip | |
| 60 | |
| 61 The following data in GFF format:: | |
| 62 | |
| 63 chr19 Nimblegen tiling_array 100000 1000051 -1.2 + . probe_name | |
| 64 chr19 Nimblegen tiling_array 100100 1000151 2.9 + . probe_name | |
| 65 | |
| 66 will be converted to WIG as shown below (Please note that a header will be added to the file):: | |
| 67 | |
| 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 | |
| 69 chr19 1000000 1000050 -1.2 | |
| 70 chr19 1000100 1000150 2.9 | |
| 71 | |
| 72 .. class:: infomark | |
| 73 | |
| 74 "Analysis name" will be shown in the UCSC Genome Browser as track name and can be defined by user. | |
| 75 | |
| 76 Viusalize chip raw intensity: | |
| 77 | |
| 78 .. image:: static/images/CARPET/ucsc2.jpg | |
| 79 | |
| 80 | |
| 81 | |
| 82 </help> | |
| 83 </tool> |