[galaxy-dev] [hg] galaxy 2813: Updated BWA and Bowtie wrapper tools so that t...

[Nate Coraor]

details:   http://www.bx.psu.edu/hg/galaxy/rev/695f28311b36
changeset: 2813:695f28311b36
user:      Kelly Vincent <kpvincent at bx.psu.edu>
date:      Thu Oct 01 13:16:43 2009 -0400
description:
Updated BWA and Bowtie wrapper tools so that the dbkey of the output is correctly assigned

4 file(s) affected in this change:

tools/sr_mapping/bowtie_wrapper.xml
tools/sr_mapping/bowtie_wrapper_code.py
tools/sr_mapping/bwa_wrapper.xml
tools/sr_mapping/bwa_wrapper_code.py

diffs (69 lines):

diff -r d31ab50dc8e0 -r 695f28311b36 tools/sr_mapping/bowtie_wrapper.xml
--- a/tools/sr_mapping/bowtie_wrapper.xml	Thu Oct 01 12:35:41 2009 -0400
+++ b/tools/sr_mapping/bowtie_wrapper.xml	Thu Oct 01 13:16:43 2009 -0400
@@ -152,7 +152,6 @@
   	      <options from_file="bowtie_indices.loc">
   	        <column name="value" index="1" />
   	        <column name="name" index="0" />
-  	        <filter type="sort_by" column="0" />
   	      </options>
   	    </param>
   	  </when>
@@ -540,4 +539,5 @@
 	--seed &lt;int&gt;       Random seed. Use &lt;int&gt; as the seed for the pseudo-random number generator. [off]
 
   </help>
+  <code file="bowtie_wrapper_code.py" />
 </tool>
diff -r d31ab50dc8e0 -r 695f28311b36 tools/sr_mapping/bowtie_wrapper_code.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_mapping/bowtie_wrapper_code.py	Thu Oct 01 13:16:43 2009 -0400
@@ -0,0 +1,15 @@
+import os
+
+def exec_before_job(app, inp_data, out_data, param_dict, tool):
+    try:
+        refFile = param_dict['refGenomeSource']['indices'].value
+        dbkey = os.path.split(refFile)[1].split('.')[0]
+        # deal with the one odd case
+        if dbkey.find('chrM') >= 0:
+            dbkey = 'equCab2'
+        out_data['output'].set_dbkey(dbkey)
+    except:
+        try:
+            refFile = param_dict['refGenomeSource']['ownFile'].dbkey
+        except:
+            out_data['output'].set_dbkey('?')     
diff -r d31ab50dc8e0 -r 695f28311b36 tools/sr_mapping/bwa_wrapper.xml
--- a/tools/sr_mapping/bwa_wrapper.xml	Thu Oct 01 12:35:41 2009 -0400
+++ b/tools/sr_mapping/bwa_wrapper.xml	Thu Oct 01 13:16:43 2009 -0400
@@ -80,7 +80,6 @@
  	  	      <options from_file="sequence_index_color.loc">
   	  	        <column name="value" index="1" />
 	  	        <column name="name" index="0" />
-	  	        <filter type="sort_by" column="0" />
 	  	      </options>
 	  	    </param>
 	  	  </when>
@@ -100,7 +99,6 @@
  	  	      <options from_file="sequence_index_base.loc">
   	  	        <column name="value" index="1" />
 	  	        <column name="name" index="0" />
- 	  	        <filter type="sort_by" column="0" />
 	  	      </options>
 	        </param>
 	      </when>
diff -r d31ab50dc8e0 -r 695f28311b36 tools/sr_mapping/bwa_wrapper_code.py
--- a/tools/sr_mapping/bwa_wrapper_code.py	Thu Oct 01 12:35:41 2009 -0400
+++ b/tools/sr_mapping/bwa_wrapper_code.py	Thu Oct 01 13:16:43 2009 -0400
@@ -4,5 +4,8 @@
     try:
         refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value
         out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0])
-    except Exception, eq:
-        out_data['output'].set_dbkey(param_dict['dbkey'])     
+    except:
+        try:
+            refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey
+        except:
+            out_data['output'].set_dbkey('?')