--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf_to_gff.xml	Thu Apr 23 18:01:45 2015 -0400
@@ -0,0 +1,92 @@
+<tool id="fml_gtf2gff" name="GTF-to-GFF" version="2.1.0">
+	<description>converter</description> 
+	<command interpreter="python">gtf_to_gff.py $inf_gtf &gt; $gff3_format 
+	</command> 
+	<inputs>
+  		<param format="gtf" name="inf_gtf" type="data" label="Convert this query" help="Provide genome annotation file in GTF."/>
+    </inputs>
+  	<outputs>
+  		<data format="gff" name="gff3_format" label="${tool.name} on ${on_string}: Converted" /> 
+  	</outputs>
+	<tests>
+       	<test>
+            <param name="inf_gtf" value="aceview_hs_37.gtf" />
+            <output name="gff3_format" file="aceview_hs_37.gff3" />
+       	</test>
+    </tests>
+  	<help>
+
+**What it does**
+
+This tool converts data from GTF to a valid GFF file (scroll down for format description).
+
+--------
+
+**Example**
+
+- The following data in GTF::
+
+	17      protein_coding  exon    7255208 7258258 .       +       .        gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
+	17      protein_coding  CDS     7256262 7256957 .       +       0        gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; protein_id "ENSP00000328352";
+	17      protein_coding  start_codon     7256262 7256264 .       +       0        gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
+	17      protein_coding  stop_codon      7256958 7256960 .       +       0        gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
+
+- Will be converted to GFF3::
+
+	##gff-version 3
+	17      protein_coding  gene    7255208 7258258 .       +       .       ID=ENSG00000213859;Name=KCTD11
+	17      protein_coding  mRNA    7255208 7258258 .       +       .       ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
+	17      protein_coding  protein 7256262 7256960 .       +       .       ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751
+	17      protein_coding  five_prime_UTR  7255208 7256261 .       +       .       Parent=ENST00000333751
+	17      protein_coding  CDS     7256262 7256960 .       +       0       Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
+	17      protein_coding  three_prime_UTR 7256961 7258258 .       +       .       Parent=ENST00000333751
+	17      protein_coding  exon    7255208 7258258 .       +       .       Parent=ENST00000333751
+
+--------
+
+**Reference**
+
+**GTF-to-GFF** is part of oqtans package and cited as [1]_.
+
+.. [1] Sreedharan VT, Schultheiss SJ, Jean G et.al., Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics (2014). `10.1093/bioinformatics/btt731`_
+
+.. _10.1093/bioinformatics/btt731: http://goo.gl/I75poH
+
+------
+
+**About formats**
+
+**GTF format** Gene Transfer Format, it borrows from GFF, but has additional structure that warrants a separate definition and format name. GTF lines have nine tab-seaparated fields::
+
+    1. seqname - The name of the sequence.
+    2. source - This indicating where the annotation came from.
+    3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
+    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 - The score field indicates a degree of confidence in the feature's existence and coordinates.
+    7. strand - Valid entries include '+', '-', or '.'
+    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.
+    9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.
+
+**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. seqid - Must be a chromosome or scaffold.
+    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.
+
+--------
+
+**Copyright**
+
+GTF-to-GFF Wrapper Version 0.6 (Apr 2015)
+
+2009-2015 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center
+
+	</help>
+</tool>