diff emboss_format_corrector.py @ 18:c2228166c035 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00"

--- a/emboss_format_corrector.py	Tue Dec 03 02:12:56 2019 +0000
+++ b/emboss_format_corrector.py	Fri Nov 20 16:49:40 2020 +0000
@@ -3,7 +3,7 @@
 
 
 # Properly set file formats before job run
-def exec_before_job( app, inp_data=None, out_data=None, tool=None, param_dict=None ):
+def exec_before_job(app, inp_data=None, out_data=None, tool=None, param_dict=None):
     # why isn't items an ordered list?
     items = out_data.items()
     items = sorted(items, key=operator.itemgetter(0))
@@ -11,7 +11,7 @@
     # normal filetype correction
     data_count = 1
     for name, data in items:
-        outputType = param_dict.get( 'out_format' + str(data_count), None )
+        outputType = param_dict.get('out_format' + str(data_count), None)
         if outputType is not None:
             if outputType == 'ncbi':
                 outputType = "fasta"
@@ -20,28 +20,28 @@
             elif outputType == 'text':
                 outputType = "txt"
             data = app.datatypes_registry.change_datatype(data, outputType)
-            app.model.context.add( data )
+            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 )
+        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.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 )
+        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.add(data)
             app.model.context.flush()
         data_count += 1