# HG changeset patch
# User yhoogstrate
# Date 1393247974 18000
# Node ID 4850787ee1d9438ddce0993fd348dd9219cbd42d
# Parent  0abd1de087031cf095d3678bc4193b43d93fbc5f
Uploaded

diff -r 0abd1de08703 -r 4850787ee1d9 featurecounts_valid_gff.xml
--- a/featurecounts_valid_gff.xml	Fri Feb 21 04:23:38 2014 -0500
+++ b/featurecounts_valid_gff.xml	Mon Feb 24 08:19:34 2014 -0500
@@ -93,7 +93,7 @@
 			</param>
 			<when value="indexed_filtered">
 				<param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
-					<options from_file="gene_sets.loc">
+					<options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
 						<column name="name"  index="0"/>
 						<column name="dbkey" index="1"/>
 						<column name="value" index="2"/>
@@ -104,7 +104,7 @@
 			</when>
 			<when value="indexed_all">
 				<param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
-					<options from_file="gene_sets.loc">
+					<options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
 						<column name="name"  index="0"/>
 						<column name="dbkey" index="1"/>
 						<column name="value" index="2"/>
diff -r 0abd1de08703 -r 4850787ee1d9 tool-data/gene_sets.loc.sample
--- a/tool-data/gene_sets.loc.sample	Fri Feb 21 04:23:38 2014 -0500
+++ b/tool-data/gene_sets.loc.sample	Mon Feb 24 08:19:34 2014 -0500
@@ -1,15 +1,18 @@
-# Because of this file, galaxy tools can access gene annotations
+# This is a sample file distributed with Galaxy that enables tools
+# to use gene/exon annotations in the GFF/GTF format. You will need
+# to add all the gene set annotations in this configuration file.
+# Because of this file, galaxy tools are able to access gene annotations
 # provided as GFF / GTF files by selecting on:
-# - Priorty (order in the file)
+# - Priorty (defined by the order in the file)
 # - Provider
 # - dbkey (reference genome id)
 # 
 # The gene_sets.loc file syntax is:
 # <name/UID> <dbkey> <path> <provider> <URL/reference*>
-#
-# *optional
+#  *optional
 # 
 # Please ensure maximally one TAB (\t) between two columns!
+# ---------------------------------------------------------
 # 
 # In case you have TWO or MORE providers PER dbkey, the one mentioned
 # first in the file, should have the "default" priority.
diff -r 0abd1de08703 -r 4850787ee1d9 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Feb 21 04:23:38 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Mon Feb 24 08:19:34 2014 -0500
@@ -1,5 +1,8 @@
-<?xml version="1.0"?>
-<table name="gene_sets" comment_char="#">
-	<columns>name, dbkey, value, provider, reference</columns>
-	<file path="tool-data/gene_sets.loc.sample" /> 
-</table>
\ No newline at end of file
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of all GFF/GTF files -->
+    <table name="gene_sets" comment_char="#">
+        <columns>name, dbkey, value, provider, reference</columns>
+        <file path="tool-data/gene_sets.loc" />
+    </table>
+</tables>
\ No newline at end of file