# HG changeset patch
# User charles-bernard
# Date 1477579890 14400
# Node ID 2b94580bcd89f3672053f2bcc2bcacdfa1cfb0c2
# Parent  4d8c94b9a6d7891eb24ad0677e103ce902866ca8
Uploaded

diff -r 4d8c94b9a6d7 -r 2b94580bcd89 data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml
--- a/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml	Thu Oct 27 10:11:12 2016 -0400
+++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml	Thu Oct 27 10:51:30 2016 -0400
@@ -33,4 +33,25 @@
    <outputs>
       <data name="out_file" format="data_manager_json"/>
   </outputs>
+
+    <help>
+<![CDATA[
+**What it does**
+
+
+  | 1. The tool asks the admin to enter a *species_name* and automatically download the last release of the corresponding gtf annotation file on Ensembl. 
+  |
+  | 2. The tool calls ALFA.py to generate the alfa indexes from this gtf file.
+  |
+  | 3. Resulting indexes are stored in the child directory *alfa_indexes/* of the dir *<galaxy_data_manager_data_path>* defined in *config/galaxy.ini*
+  |
+  | 4. Finally, the tool add the new entry to the table *alfa_indexes.loc*. This .loc file is where the data table *alfa_indexes* points, as defined in *config/shed_tool_data_table.conf.xml*
+  |
+  | 5. At the end of the process, when a user will use `alfa`_ , the built-in indexes corresponding to the *species_name* will be available
+
+  .. _alfa: https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa
+
+]]>
+     </help>
+
 </tool>