diff tools/emboss_5/emboss_format_corrector.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/emboss_5/emboss_format_corrector.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,53 @@
+#EMBOSS format corrector
+
+import operator
+#from galaxy import datatypes
+
+#Properly set file formats after job run
+def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr):
+#Properly set file formats before job run
+#def exec_before_job(trans, inp_data, out_data, param_dict,tool):
+    #why isn't items an ordered list?
+    items = out_data.items()
+    #lets sort it ourselves....
+    items = sorted(items, key=operator.itemgetter(0))
+    #items is now sorted...
+    
+    #normal filetype correction
+    data_count=1
+    for name, data in items:
+        outputType = param_dict.get( 'out_format'+str(data_count), None )
+        #print "data_count",data_count, "name", name, "outputType", outputType
+        if outputType !=None:
+            if outputType == 'ncbi':
+                outputType = "fasta"
+            elif outputType == 'excel':
+                outputType = "tabular"
+            elif outputType == 'text':
+                outputType = "txt"
+            data = app.datatypes_registry.change_datatype(data, outputType)
+            app.model.context.add( data )
+            app.model.context.flush()
+        data_count+=1
+    
+    #html filetype correction
+    data_count=1
+    for name, data in items:
+        wants_plot = param_dict.get( 'html_out'+str(data_count), None )
+        ext = "html"
+        if wants_plot == "yes":
+            data = app.datatypes_registry.change_datatype(data, ext)
+            app.model.context.add( data )
+            app.model.context.flush()
+        data_count+=1
+    
+    #png file correction
+    data_count=1
+    for name, data in items:
+        wants_plot = param_dict.get( 'plot'+str(data_count), None )
+        ext = "png"
+        if wants_plot == "yes":
+            data = app.datatypes_registry.change_datatype(data, ext)
+            app.model.context.add( data )
+            app.model.context.flush()
+        data_count+=1