# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1414061619 18000
# Node ID df236b5e29857c42b7fb83f490f5dbc3433a0443
# Parent  8a04c5e6bfe33f7566e299b03bc4d4ce9b541a0f
Change reference to extra_files_path

diff -r 8a04c5e6bfe3 -r df236b5e2985 lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
--- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml	Tue Oct 14 14:27:38 2014 -0400
+++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml	Thu Oct 23 05:53:39 2014 -0500
@@ -1,6 +1,6 @@
 <tool id="tabular_to_dbnsfp" name="Convert tabular to dbnsfp" version="1.0.0">
   <description></description> 
-  <command interpreter="python">tabular_to_dbnsfp.py $input $dbnsfp.dataset.extra_files_path/dbNSFP.gz</command>
+  <command interpreter="python">tabular_to_dbnsfp.py $input $dbnsfp.extra_files_path/dbNSFP.gz</command>
   <inputs>
       <param format="tabular" name="input" type="data" label="Choose a dbnsfp tabular file"/>
    </inputs>
diff -r 8a04c5e6bfe3 -r df236b5e2985 lib/galaxy/datatypes/snpsift_dbnsfp.py
--- a/lib/galaxy/datatypes/snpsift_dbnsfp.py	Tue Oct 14 14:27:38 2014 -0400
+++ b/lib/galaxy/datatypes/snpsift_dbnsfp.py	Thu Oct 23 05:53:39 2014 -0500
@@ -11,7 +11,7 @@
 
 class SnpSiftDbNSFP( Text ):
     """Class describing a dbNSFP database prepared fpr use by SnpSift dbnsfp """
-    MetadataElement( name='reference_name', default='dbSNFP' , desc='Reference Name', readonly=False, visible=True, set_in_upload=True, no_value='dbSNFP' )
+    MetadataElement( name='reference_name', default='dbSNFP' , desc='Reference Name', readonly=True, visible=True, set_in_upload=True, no_value='dbSNFP' )
     MetadataElement( name="bgzip", default=None, desc="dbNSFP bgzip", readonly=True, visible=True, no_value=None )
     MetadataElement( name="index", default=None, desc="Tabix Index File", readonly=True, visible=True, no_value=None)
     MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[] )
@@ -55,12 +55,10 @@
         f.close()
     def set_meta( self, dataset, overwrite=True, **kwd ):
         try:
-            # Text.set_meta( self, dataset, **kwd)
             efp = dataset.extra_files_path
             if os.path.exists(efp):
                 flist = os.listdir(efp)
                 for i,fname in enumerate(flist):
-                    # log.info("set_meta fname: %d %s" % (i,fname))
                     if fname.endswith('.gz'):
                         dataset.metadata.bgzip = fname
                         try: