<tool id="gff to bed wiggle" name="Gff2Wig" version="1.1.0">
  <description>easy UCSC visualization of your raw-data</description>
  <command interpreter="perl">gff2bed_v2.pl $input $col3 >$output</command>
  <inputs>
    <param format="gff" name="input" type="data" label="Source file"/>
    <param name="col3" size="20" type="text" value="Analysis" label="Analysis name"/>
  </inputs>
  <outputs>
     <data format="bed" name="output" file="wig-gff2bed.dat"/>
  </outputs>

  <tests>
    <test>
      <param name="input" value="1.gff"/>
      <output name="output" file="wig-gff2bed.dat"/> 
    </test>
  </tests>
  <help>
.. class:: infomark

**What it does**

This tool converts data from GFF format to WIGGLE format. This format allows the visuallization of raw intensity signals into the UCSC Genome Browser.

PLEASE, for more detailed information refer to the CARPET user Manual:
click to download_ it.

.. _download: /static/example_file/CARPET_userManual.zip

--------

.. class:: infomark

About formats

**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:

1. seqname - Must be a chromosome or scaffold.
2. source - The program that generated this feature.
3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. end - The ending position of the feature (inclusive).
6. score - A score or signal. If there is no score value, enter ".".
7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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 '.'.
9. group - All lines with the same group are linked together into a single item.

--------


**Example**


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.


Click here_ to download a GFF file example.

.. _here: /static/example_file/GFF_file_norm.txt.zip	

The following data in GFF format::

    chr19  Nimblegen  tiling_array  100000  1000051  -1.2	 +   .  probe_name
    chr19  Nimblegen  tiling_array  100100  1000151   2.9	 +   .  probe_name
    
will be converted to WIG as shown below (Please note that a header will be added to the file)::

    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
    chr19   1000000  1000050   -1.2
    chr19   1000100  1000150    2.9

.. class:: infomark

"Analysis name" will be shown in the UCSC Genome Browser as track name and can be defined by user.

Viusalize chip raw intensity:

.. image:: static/images/CARPET/ucsc2.jpg

  
  
  </help>
</tool>
