view fml_gff_groomer/galaxy/gff_id_mapper.xml @ 0:79726c328621 default tip

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

<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 ([e-mail])
</help>
</tool>