From 778088bba9b8b9f88e9b65b5f9dc91f014aec8a3 Mon Sep 17 00:00:00 2001
From: Kelly Vincent <kpvincent@bx.psu.edu>
Date: Tue, 17 May 2011 12:05:07 -0400
Subject: [PATCH] Modified Tophat wrapper so dbkey will be properly set both
 for built-in and history references

---
 tools/ngs_rna/tophat_wrapper.xml | 78 ++++++++++++++++++++++++++++++--
 1 file changed, 74 insertions(+), 4 deletions(-)

diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index 45085552099..c8f451781b4 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="tophat" name="Tophat" version="1.2.0">
+<tool id="tophat" name="Tophat" version="1.2.1">
     <description>Find splice junctions using RNA-seq data</description>
     <requirements>
         <requirement type="package">tophat</requirement>
@@ -100,7 +100,7 @@
                     --seg-length=$singlePaired.pParams.seg_length
                     --library-type=$singlePaired.pParams.library_type
                     
-		    ## Indel search.
+                    ## Indel search.
                     #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
                         --allow-indels
                         --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
@@ -386,6 +386,23 @@
                       ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
                 ) 
             </filter>
+            <actions>
+              <conditional name="refGenomeSource.genomeSource">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                    </option>
+                  </action>
+                </when>
+                <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+                  </action>
+                </when>
+              </conditional>
+            </actions>
         </data>
         <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
             <filter>
@@ -396,9 +413,62 @@
                       ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
                 )
             </filter>
+            <actions>
+              <conditional name="refGenomeSource.genomeSource">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                    </option>
+                  </action>
+                </when>
+                <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+                  </action>
+                </when>
+              </conditional>
+            </actions>
+        </data>
+        <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
+            <actions>
+              <conditional name="refGenomeSource.genomeSource">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                    </option>
+                  </action>
+                </when>
+                <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+                  </action>
+                </when>
+              </conditional>
+            </actions>
+        </data>
+        <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
+            <actions>
+              <conditional name="refGenomeSource.genomeSource">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                    </option>
+                  </action>
+                </when>
+                <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+                  </action>
+                </when>
+              </conditional>
+            </actions>
         </data>
-        <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/>
-        <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/>
     </outputs>
 
     <tests>