Mercurial > repos > charles-bernard > data_manager_build_alfa_indexes

changeset 8:2b94580bcd89 draft

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Uploaded
author charles-bernard
date Thu, 27 Oct 2016 10:51:30 -0400
parents 4d8c94b9a6d7
children 10443d81d972
files data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml
diffstat 1 files changed, 21 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- 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>