--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/bed2gff.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,89 @@
+<tool id="bed2gff1" name="BED-to-GFF" version="2.0.0">
+  <description>converter</description>
+  <command interpreter="python">bed_to_gff_converter.py $input $out_file1</command>
+  <inputs>
+    <param format="bed" name="input" type="data" label="Convert this query"/>
+  </inputs>
+  <outputs>
+    <data format="gff" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="9.bed"/>
+      <output name="out_file1" file="bed2gff_out.gff"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This tool converts data from BED format to GFF format (scroll down for format description).
+
+--------
+
+**Example**
+
+The following data in BED format::
+
+	chr28	346187	388197	BC114771	0	+	346187	388197	0	9	144,81,115,63,155,96,134,105,112,	0,24095,26190,31006,32131,33534,36994,41793,41898,
+
+Will be converted to GFF (**note** that the start coordinate is incremented by 1)::
+
+	##gff-version 2
+	##bed_to_gff_converter.py
+
+	chr28	bed2gff	mRNA	346188	388197	0	+	.	mRNA BC114771;
+	chr28	bed2gff	exon	346188	346331	0	+	.	exon BC114771;
+	chr28	bed2gff	exon	370283	370363	0	+	.	exon BC114771;
+	chr28	bed2gff	exon	372378	372492	0	+	.	exon BC114771;
+	chr28	bed2gff	exon	377194	377256	0	+	.	exon BC114771;
+	chr28	bed2gff	exon	378319	378473	0	+	.	exon BC114771;
+	chr28	bed2gff	exon	379722	379817	0	+	.	exon BC114771;
+	chr28	bed2gff	exon	383182	383315	0	+	.	exon BC114771;
+	chr28	bed2gff	exon	387981	388085	0	+	.	exon BC114771;
+	chr28	bed2gff	exon	388086	388197	0	+	.	exon BC114771;
+
+
+------
+
+.. class:: informark
+
+**About formats**
+
+**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:
+
+The first three BED fields (required) are::
+
+    1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
+    2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
+    3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
+
+The additional BED fields (optional) are::
+
+    4. name - The name of the BED line.
+    5. score - A score between 0 and 1000.
+    6. strand - Defines the strand - either '+' or '-'.
+    7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
+    8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
+    9. reserved - This should always be set to zero.
+   10. blockCount - The number of blocks (exons) in the BED line.
+   11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
+   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.
+   13. expCount - The number of experiments.
+   14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
+   15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.
+
+**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 between 0 and 1000. 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.
+
+</help>
+</tool>