From e42b3e1b01ee0e41f0244afabc2264784abe68cf Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 22 Nov 2010 16:02:43 -0500
Subject: [PATCH] Update bowtie tool output dataset actions to reference
 columns in the new location file style.

FIXME: Tool output actions need to be made data_table aware.
---
 tools/sr_mapping/bowtie_color_wrapper.xml | 12 ++----------
 tools/sr_mapping/bowtie_wrapper.xml       | 12 ++----------
 2 files changed, 4 insertions(+), 20 deletions(-)

diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml
index 2a7c73d0afa..0a411bf742d 100644
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -317,21 +317,13 @@
         <conditional name="refGenomeSource.genomeSource">
           <when value="indexed">
             <action type="metadata" name="dbkey">
-              <option type="from_file" name="bowtie_indices_color.loc" column="0" offset="0">
+              <option type="from_file" name="bowtie_indices_color.loc" column="1" offset="0">
                 <filter type="param_value" column="0" value="#" filter_by="startswith" keep="False"/>
-                <filter type="param_value" ref="refGenomeSource.index" column="1"/>
+                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
               </option>
             </action>
           </when>
         </conditional>
-        <!-- Special casing equCab2chrM to equCab2 -->
-        <action type="metadata" name="dbkey">
-          <option type="from_param" name="refGenomeSource.genomeSource" column="0" offset="0">
-            <filter type="insert_column" column="0" value="equCab2chrM"/>
-            <filter type="insert_column" column="0" value="equCab2"/>
-            <filter type="metadata_value" ref="output" name="dbkey" column="1" />
-          </option>
-        </action>
       </actions>
     </data>
   </outputs>
diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml
index ad5beb982d5..4f4deb86bd4 100644
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -300,21 +300,13 @@
         <conditional name="refGenomeSource.genomeSource">
           <when value="indexed">
             <action type="metadata" name="dbkey">
-              <option type="from_file" name="bowtie_indices.loc" column="0" offset="0">
+              <option type="from_file" name="bowtie_indices.loc" column="1" offset="0">
                 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                <filter type="param_value" ref="refGenomeSource.index" column="1"/>
+                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
               </option>
             </action>
           </when>
         </conditional>
-        <!-- Special casing equCab2chrM to equCab2 -->
-        <action type="metadata" name="dbkey">
-          <option type="from_param" name="refGenomeSource.genomeSource" column="0" offset="0">
-            <filter type="insert_column" column="0" value="equCab2chrM"/>
-            <filter type="insert_column" column="0" value="equCab2"/>
-            <filter type="metadata_value" ref="output" name="dbkey" column="1" />
-          </option>
-        </action>
       </actions>
     </data>
   </outputs>