# HG changeset patch
# User charles-bernard
# Date 1479547486 18000
# Node ID 4f70c9afd89d55431e2c9869c2d81c0ec3d873ad
# Parent  66e35b650256afc680b476a2d0a7c78639945518
Uploaded

diff -r 66e35b650256 -r 4f70c9afd89d data_manager_build_alfa_indexes/.shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_build_alfa_indexes/.shed.yml	Sat Nov 19 04:24:46 2016 -0500
@@ -0,0 +1,13 @@
+categories:
+- Data Managers
+description: A tool to build ALFA indexes from automatically downloaded gtf annotation file
+long_description: |
+	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 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 adds 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 (https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa), the built-in indexes corresponding to the 'species_name' will be available
+name: data_manager_build_alfa_indexes
+owner: charles_bernard
+remote_repository_url: https://github.com/charles-bernard/Galaxy_tools/tree/master/data_manager_build_alfa_indexes
+type: unrestricted
\ No newline at end of file
diff -r 66e35b650256 -r 4f70c9afd89d 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	Wed Nov 16 12:37:49 2016 -0500
+++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml	Sat Nov 19 04:24:46 2016 -0500
@@ -7,7 +7,7 @@
       <requirement type="package" version="1.4">matplotlib</requirement>
   </requirements>
   
-  <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" $__tool_directory__</command>
+  <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" "$__tool_directory__"</command>
 
   <inputs>
     <conditional name="reference_source">