# HG changeset patch
# User Lance Parsons <lparsons@princeton.edu>
# Date 1346446242 14400
# Node ID c6d73933f601d1ef9bf2905c80bbb43ba2a406d3
# Parent  8f0f896ec5276801d96e2315835bf5e9a4b26459
Fixed issues with tool shed parsing

diff -r 8f0f896ec527 -r c6d73933f601 htseq-count.xml
--- a/htseq-count.xml	Fri Aug 31 15:23:53 2012 -0400
+++ b/htseq-count.xml	Fri Aug 31 16:50:42 2012 -0400
@@ -79,7 +79,7 @@
                     <when value="cached">
                         <param name="ref_file" type="select" label="Using reference genome">
                             <options from_data_table="sam_fa_indexes">
-                                <filter type="data_meta" key="dbkey" ref="samfile" column="value"/>
+                                <filter type="data_meta" key="dbkey" ref="samfile" column="3"/>
                             </options>
                             <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                         </param>
diff -r 8f0f896ec527 -r c6d73933f601 sam_fa_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_fa_indices.loc.sample	Fri Aug 31 16:50:42 2012 -0400
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a sam_fa_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The sam_fa_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#index	<seq>	<location>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/sam/, 
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.loc file should include an entry per line for 
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#index	hg19	/depot/data2/galaxy/sam/hg19.fa
diff -r 8f0f896ec527 -r c6d73933f601 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Aug 31 16:50:42 2012 -0400
@@ -0,0 +1,8 @@
+<!-- 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 SAMTools indexes and other files -->
+    <table name="sam_fa_indexes" comment_char="#">
+        <columns>line_type, value, path</columns>
+        <file path="tool-data/sam_fa_indices.loc" />
+    </table>
+</tables>