diff fml_gff_converter_programs/galaxy/bed_to_gff3.xml @ 0:ed53dca1c6ff

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fml_gff_converter_programs/galaxy/bed_to_gff3.xml	Tue Jun 07 17:26:20 2011 -0400
@@ -0,0 +1,84 @@
+<tool id="fml_bed2gff" name="BED_to_GFF3" version="1.0.0">
+	<description>converter</description>
+	<command interpreter="python">bed_to_gff3_converter.py $inf_bed > $gff_format 
+	</command> 
+	<inputs>
+  		<param format="bed" name="inf_bed" type="data" label="Convert this query" help="Please look at About format section."/>
+    </inputs>
+  	<outputs>
+  		<data format="gff3" name="gff_format" /> 
+  	</outputs>
+	<tests>
+        <test>
+                <param name="inf_bed" value="ccds_genes.bed" />
+                <output name="gff_format" file="ccds_genes.gff3" />
+        </test>
+        <test>
+                <param name="inf_bed" value="hs_2009.bed" />
+                <output name="gff_format" file="hs_2009.gff3" />
+        </test>
+        </tests>
+  	<help>
+
+**What it does**
+
+This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format.
+
+--------
+
+**Example**
+
+- The following data in UCSC Wiggle BED format::
+
+	chr1    11873   14409   uc001aaa.3      0       +       11873   11873   0       3       354,109,1189,   0,739,1347,
+
+- Will be converted to GFF3 format::
+
+	##gff-version 3
+	chr1    bed2gff gene    11874   14409   0       +       .       ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3
+	chr1    bed2gff transcript      11874   14409   0       +       .       ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3
+	chr1    bed2gff exon    11874   12227   0       +       .       Parent=uc001aaa.3
+	chr1    bed2gff exon    12613   12721   0       +       .       Parent=uc001aaa.3
+	chr1    bed2gff exon    13221   14409   0       +       .       Parent=uc001aaa.3
+
+--------
+
+**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.
+
+**GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields:
+
+    1. seqid - Must be a chromosome or scaffold or contig.
+    2. source - The program that generated this feature.
+    3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". 
+    4. start - The starting position of the feature in the sequence. The first base is numbered 1.
+    5. stop - 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. phase - 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. attributes - All lines with the same group are linked together into a single item.
+
+--------
+
+This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan ([e-mail])
+	</help>
+</tool>