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+++ b/tools/filters/gff2bed.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,87 @@
+<tool id="gff2bed1" name="GFF-to-BED" version="1.0.1">
+  <description>converter</description>
+  <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
+  <inputs>
+    <param format="gff" name="input" type="data" label="Convert this query"/>
+  </inputs>
+  <outputs>
+    <data format="bed" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="5.gff" ftype="gff"/>
+      <output name="out_file1" file="gff2bed_out.bed"/>
+    </test>
+    <test>
+      <param name="input" value="gff2bed_in2.gff" ftype="gff"/>
+      <output name="out_file1" file="gff2bed_out2.bed"/>
+    </test>
+    <test>
+      <!-- Test conversion of gff3 file. -->
+      <param name="input" value="5.gff3" ftype="gff"/>
+      <output name="out_file1" file="gff2bed_out3.bed"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This tool converts data from GFF format to BED format (scroll down for format description).
+
+--------
+
+**Example**
+
+The following data in GFF format::
+
+    chr22  GeneA  enhancer  10000000  10001000  500	 +   .  TGA
+    chr22  GeneA  promoter  10010000  10010100  900	 +   .  TGA
+
+Will be converted to BED (**note** that 1 is subtracted from the start coordinate)::
+
+    chr22   9999999  10001000   enhancer   0   +
+    chr22  10009999  10010100   promoter   0   +
+
+------
+
+.. class:: infomark
+
+**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>