# HG changeset patch
# User Dave Bouvier <dave@bx.psu.edu>
# Date 1386784472 18000
# Node ID dddde948c3e5fe03701bd5e8b7d11241da17a15d
# Parent  44a18a94d7a9ba97e0872ad9f90b7e8f96e005d9
Update samtools_mpileup to use the fasta_indexes data table.

diff -r 44a18a94d7a9 -r dddde948c3e5 samtools_mpileup.xml
--- a/samtools_mpileup.xml	Mon Aug 26 14:23:36 2013 -0400
+++ b/samtools_mpileup.xml	Wed Dec 11 12:54:32 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="samtools_mpileup" name="MPileup" version="0.0.1">
+<tool id="samtools_mpileup" name="MPileup" version="0.0.2">
   <description>SNP and indel caller</description>
   <requirements>
       <requirement type="package" version="0.1.18">samtools</requirement>
@@ -59,22 +59,22 @@
       </param>
       <when value="cached">
         <repeat name="input_bams" title="BAM file" min="1">
-            <param name="input_bam" type="data" format="bam" label="BAM file">
-              <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
-            </param>
+          <param name="input_bam" type="data" format="bam" label="BAM file">
+            <validator type="unspecified_build" />
+            <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          </param>
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="sam_fa_indexes">
-            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> 
+          <options from_data_table="fasta_indexes">
+            <!-- <filter type="data_meta" ref="input_bam" key="dbkey" column="1" /> does not yet work in a repeat...-->
           </options>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <repeat name="input_bams" title="BAM file" min="1">
-            <param name="input_bam" type="data" format="bam" label="BAM file" >
-              <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-            </param>
+          <param name="input_bam" type="data" format="bam" label="BAM file">
+            <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." />
+          </param>
         </repeat>
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
diff -r 44a18a94d7a9 -r dddde948c3e5 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 11 12:54:32 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 44a18a94d7a9 -r dddde948c3e5 tool-data/sam_fa_indices.loc.sample
--- a/tool-data/sam_fa_indices.loc.sample	Mon Aug 26 14:23:36 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 44a18a94d7a9 -r dddde948c3e5 tool-data/tool_data_table_conf.xml.sample
--- a/tool-data/tool_data_table_conf.xml.sample	Mon Aug 26 14:23:36 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<!-- 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>
\ No newline at end of file
diff -r 44a18a94d7a9 -r dddde948c3e5 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 11 12:54:32 2013 -0500
@@ -0,0 +1,7 @@
+<!-- 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>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>