<tool id="Annotation_Expr" name="ENO" version="1.0.0">
  <description>Expression NOtator</description>
  <command interpreter="perl">annotation_expr_intron.pl $input1 $input2 $output</command>
  <inputs>
    <param format="tabular" name="input1" type="data" label="Expression file"/>
    <param format="tabular" name="input2" type="data" label="Annotation table"/>
  </inputs>
  <outputs>
     <data format="tabular" name="output"/>
  </outputs>
	<help>
 .. class:: infomark

**What it does**

ENO assigns each exon of a transcript the relative matching probes of the array. If a probe matches with more than one transcript, it is associated to every transcript.

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 was 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.**


--------

.. 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


---------

.. class:: infomark

**How does it work?**

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



	</help>
</tool>