<tool id="Annotation_RefSeq" name="GIN" version="1.3.0">
  <description>Gene Intervals Notator</description>
  <command interpreter="perl">MapToExon_RefSeqMat_new.pl $input1 $input2 $promoter $3prime $priority $output</command>
  <inputs>
    <param format="tabular" name="input1" type="data" label="GFF file"/>
    <param format="tabular" name="input2" type="data" label="Annotation table"/>
   	<param name="promoter" type="integer" size="10" value="-2000" label="Promoter definition (bp)"/>
   	<param name="3prime" type="integer" size="10" value="2000" label="3prime extension (bp)"/>
   	<param name="priority" type="select" label="Annotation priority">
    	  <option value="prom">promoter</option>
    	  <option value="gene">gene</option>
   	</param>

  </inputs>
  <outputs>
     <data format="tabular" name="output"/>
  </outputs>

	<help>
 .. class:: infomark

**What it does**

GIN annotates peak queries (GFF files) with user defined transcript-annotation-tables (e.g. RefSeq, UCSC genes, Ensembl Genes etc).
It calculates the relative position of the peack with respect to the associated features (e.g. promoter, exon, intron, intergenic)

PLEASE, for more detailed information refer to the CARPET user Manual:
click to download_ it.

.. _download: /static/example_file/CARPET_userManual.zip

--------

.. class:: warningmark

**Annotation Table**

Annotation table is directly downloadable from **"Get Data"** section (**"UCSC Main table browser"** link).
Pay attention to choose the right output format (**"all field from selected table"**) and check **"send output to Galaxy"**.

It is possible to download many different annotation tables coming from different organisms and database such as RefSeq, UCSC gene, FlyBase, EST, etc etc...

**All annotation tables must have headers.**

Click here_ to download an Annotation Table file example.

.. _here: /static/example_file/UCSC_hs_refGene_chr19.zip

--------

.. class:: warningmark

**Custom annotation table**

  .. class:: infomark 

 
  **About format**
 
  Annotation table format must be the same downlodable from UCSC. In the specific case of this tool the following fields must be present:
 
  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).
  4. **name** - The name of the BED line.
  5. **strand** - Defines the strand - either + or - .
  6. **blockCount** - The number of blocks (exons) in the BED line.
  7. **blockSizes** - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
  8. **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.
 

The table **must** have headers


--------

**Options**

- **Promoter definition:** extent of TSS (Trascription Starting Site) upstream sequence in base pairs.
- **Annotaion priority:**
	- if **promoter**: GIN tries to locate a peak in a promoter locus as first choice. If more than one promoter is found, the peak is associated to the closer transcriptional unit
	- if **gene**: GIN tries to locate a peak in an exon as first choice. 

--------

**How does it work?**

**- Floowchart**

.. image:: static/images/CARPET/floowchart.png


**- Output**

.. image:: static/images/CARPET/output_ann.png


	</help>
</tool>
