# HG changeset patch
# User Dave Bouvier <dave@bx.psu.edu>
# Date 1386181478 18000
# Node ID beab768feb9202e57ff8c143a709af13a1d6e8ea
# Parent  2d6a90609943261c47f935418368d30017db0502
Update to the new data table specification.

diff -r 2d6a90609943 -r beab768feb92 cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Tue Oct 22 11:03:02 2013 -0400
+++ b/cuffdiff_wrapper.xml	Wed Dec 04 13:24:38 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="cuffdiff" name="Cuffdiff" version="0.0.6">
+<tool id="cuffdiff" name="Cuffdiff" version="0.0.7">
     <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 -->
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
     <requirements>
@@ -33,7 +33,7 @@
                     $bias_correction.seq_source.ref_file
                 #else:
                     ## Built-in genome.
-                    ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
+                    ${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')}
                 #end if
             #end if
 
@@ -89,7 +89,14 @@
                     <option value="cached">Locally cached</option>
                     <option value="history">History</option>
                   </param>
-                  <when value="cached"></when>
+                  <when value="cached">
+                    <param name="index" type="select" label="Using reference genome">
+                      <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
+                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+                      </options>
+                    </param>
+                  </when>
                   <when value="history">
                       <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                   </when>
diff -r 2d6a90609943 -r beab768feb92 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Wed Dec 04 13:24:38 2013 -0500
@@ -0,0 +1,29 @@
+#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_new_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_new_indices.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the sam_fa_new_indices.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your sam_fa_new_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:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 2d6a90609943 -r beab768feb92 tool-data/sam_fa_indices.loc.sample
--- a/tool-data/sam_fa_indices.loc.sample	Tue Oct 22 11:03:02 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#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 2d6a90609943 -r beab768feb92 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Dec 04 13:24:38 2013 -0500
@@ -0,0 +1,4 @@
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>