--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carpet-src-1/tools/CARPET/annotation_expr.xml	Tue Jun 07 16:50:41 2011 -0400
@@ -0,0 +1,74 @@
+<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>