--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fml_gff_groomer/galaxy/gff_id_mapper.xml	Tue Jun 07 17:29:24 2011 -0400
@@ -0,0 +1,75 @@
+<tool id="gff_parent_child_relation" name="Examine" version="1.0.0">
+  <description>Parent-Child relation in GFF file</description>
+  <command interpreter="python"> 
+        gff_id_mapper.py
+		$gff_input
+		> $idmapping
+    </command>
+  <inputs>
+    <param format="gff3" name="gff_input" type="data" label="Genome annotation in GFF3 format" help="Genome annotation in GFF3 format describing the known gene structures and other features for the provided genome."/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="idmapping" label="Parent-child relation in GFF file" />
+  </outputs>
+		<tests>
+    		<test>
+            	<param name="gff_input" value="Feature_ID_mapping_W.gff3" />
+            	<output name="idmapping" file="Feature_ID_mapping_W.txt" />
+            </test>
+    		<test>
+            	<param name="gff_input" value="Aly_JGI.gff3" />
+            	<output name="idmapping" file="Feature_ID_mapping_R.txt" />
+            </test>
+        </tests>
+  <help>
+
+**What it does** 
+
+This tool provides the features(gene, mRNA, UTR's, exon, CDS etc) relationship based on their identifier mapping in a given GFF file.
+
+--------
+
+**Example**
+
+- The features ID mapping in the following data in GFF format::
+
+	##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  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
+
+- Will be displayed as::
+
+	FIRST level feature(s):
+		('protein_coding', 'gene')
+
+	SECOND level feature(s):
+		('protein_coding', 'mRNA')
+	
+	THIRD level feature(s):
+		('protein_coding', 'CDS'), ('protein_coding', 'exon'), ('protein_coding', 'five_prime_UTR'), ('protein_coding', 'three_prime_UTR')
+
+--------
+
+**About formats**
+
+**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.
+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 (vipin.ts@tuebingen.mpg.de)
+</help>
+</tool>