--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carpet-src-1/tools/CARPET/gff2bed_v2.xml	Tue Jun 07 16:50:41 2011 -0400
@@ -0,0 +1,83 @@
+<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>