<tool id="gff_available_limits" name="FeatureScan" version="1.0.0">
  <description>gives an overview about GFF file content</description>
  <command interpreter="python"> 
        gff_available_limits.py
		$gff_input
		> $overview
    </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="overview" label="Feature contents in GFF file" />
  </outputs>
    	<tests>
    		<test>
            	<param name="gff_input" value="GFF_2_Source.gff3" />
            	<output name="overview" file="GFF_2_Source_FeatureScan.txt" />
            </test>
    	</tests>
  <help>

**What it does** 

This tool provides an overview of available contig identifiers, sources and feature types and their corresponding counts from a given GFF file.

--------

**Example**

- The features ID mapping in the following data in GFF format::

	##gff-version 3
	scaffold_1      JGI_Filtered    gene    33131338        33131726        .       -       .       ID=scaffold_105720.1;Name=scaffold_105720.1
	scaffold_1      JGI_Filtered    mRNA    33131338        33131726        .       -       .       ID=Transcript:924439;Name=Transcript:924439;Parent=scaffold_105720.1
	scaffold_1      JGI_Filtered    three_prime_UTR 33131338        33131357        .       -       .       ID=three_prime_UTR:924439;Parent=Transcript:924439
	scaffold_1      JGI_Filtered    exon    33131338        33131654        .       -       .       ID=exon:924439;Parent=Transcript:924439
	scaffold_1      JGI_Filtered    CDS     33131358        33131654        .       -       0       ID=CDS:924439;Parent=Transcript:924439;Name=scaffold_105720.1
	scaffold_1      JGI_Filtered    exon    33131703        33131726        .       -       .       ID=exon:924439;Parent=Transcript:924439
	scaffold_1      JGI_Filtered    CDS     33131703        33131705        .       -       0       ID=CDS:924439;Parent=Transcript:924439;Name=scaffold_105720.1
	scaffold_1      JGI_Filtered    five_prime_UTR  33131706        33131726        .       -       .       ID=five_prime_UTR:924439;Parent=Transcript:924439
	Chr4    TAIR9   gene    1180    1536    .       -       .       ID=AT4G00005;Note=protein_coding_gene;Name=AT4G00005
	Chr4    TAIR9   mRNA    1180    1536    .       -       .       ID=AT4G00005.1;Parent=AT4G00005;Name=AT4G00005.1;Index=1
	Chr4    TAIR9   protein 1180    1536    .       -       .       ID=AT4G00005.1-Protein;Name=AT4G00005.1;Derives_from=AT4G00005.1
	Chr4    TAIR9   CDS     1180    1536    .       -       0       Parent=AT4G00005.1,AT4G00005.1-Protein;
	Chr4    TAIR9   exon    1180    1536    .       -       .       Parent=AT4G00005.1

- Will be displayed as::

	Chromosome identifier(s) and corresponding count:
		Chr4	5
		scaffold_1	8

	Source(s) of feature and corresponding count:
		JGI_Filtered	8
		TAIR9	5

	Feature type(s) and corresponding count:
		gene	2
		mRNA	2
		five_prime_UTR	1
		three_prime_UTR	1
		exon	3
		CDS	3
		protein	1

	Unique combination of Feature type(s), Source(s) and corresponding count:
		JGI_Filtered, CDS       2
		JGI_Filtered, exon      2
		JGI_Filtered, five_prime_UTR    1
		JGI_Filtered, gene      1
		JGI_Filtered, mRNA      1
		JGI_Filtered, three_prime_UTR 1
		TAIR9, CDS      1
		TAIR9, exon     1
		TAIR9, protein	1
		TAIR9, mRNA	1
		TAIR9, gene	1
	
--------

**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>