From 5911f50dbef037c35943f21062e53d6f65ef9725 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 18 May 2016 13:37:56 +0200
Subject: [PATCH] Fix PEP8 for biotools PR

---
 lib/galaxy/datatypes/interval.py           | 2 +-
 lib/galaxy/datatypes/qualityscore.py       | 2 ++
 lib/galaxy/tools/parameters/basic.py       | 3 +--
 lib/galaxy/webapps/galaxy/api/biotools.py  | 3 ++-
 lib/galaxy/webapps/galaxy/api/datatypes.py | 1 -
 lib/galaxy/webapps/galaxy/api/tools.py     | 3 +--
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index ffb358880e10..5a1acfca0425 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -1446,7 +1446,7 @@ class ENCODEPeak( Interval ):
     This format is used to provide called peaks of signal enrichment based on
     pooled, normalized (interpreted) data. It is a BED6+4 format.
     '''
-    edam_format = "format_3612"   
+    edam_format = "format_3612"
     file_ext = "encodepeak"
     column_names = [ 'Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'SignalValue', 'pValue', 'qValue', 'Peak' ]
     data_sources = { "data": "tabix", "index": "bigwig" }
diff --git a/lib/galaxy/datatypes/qualityscore.py b/lib/galaxy/datatypes/qualityscore.py
index 9b7a522d4540..15d14f944156 100644
--- a/lib/galaxy/datatypes/qualityscore.py
+++ b/lib/galaxy/datatypes/qualityscore.py
@@ -15,6 +15,7 @@ class QualityScore ( data.Text ):
     edam_data = "data_2048"
     edam_format = "format_3606"
 
+
 class QualityScoreSOLiD ( QualityScore ):
     """
     until we know more about quality score formats
@@ -122,6 +123,7 @@ class QualityScoreSolexa ( QualityScore ):
     file_ext = "qualsolexa"
     edam_format = "format_3608"
 
+
 class QualityScoreIllumina ( QualityScore ):
     """
     until we know more about quality score formats
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index aacd287460f4..cede7e920966 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2038,8 +2038,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
         all_edam_data = self._datatypes_registery( trans, self.tool ).edam_data
         edam_formats = map(lambda ext: all_edam_formats.get(ext, None),
                            extensions)
-        edam_data = map(lambda ext: all_edam_data.get(ext, None),
-                           extensions)
+        edam_data = map(lambda ext: all_edam_data.get(ext, None), extensions)
 
         d['extensions'] = extensions
         d['edam'] = {'edam_formats': edam_formats, 'edam_data': edam_data}
diff --git a/lib/galaxy/webapps/galaxy/api/biotools.py b/lib/galaxy/webapps/galaxy/api/biotools.py
index 17ddb4c22aef..f1310aaf6b3d 100644
--- a/lib/galaxy/webapps/galaxy/api/biotools.py
+++ b/lib/galaxy/webapps/galaxy/api/biotools.py
@@ -4,6 +4,7 @@
 import logging
 log = logging.getLogger( __name__ )
 
+
 def json_formater(fonc):
     @functools.wraps(fonc)
     def innerfunc(cl, trans, id, **kwd):
@@ -97,7 +98,7 @@ def format_description(description):
         else:
             return description[0].upper() + description[1:size] + '.'
     except IndexError:
-        raise  description
+        raise description
 
 
 def get_source_registry(tool_id):
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index 7d9c86b24022..ec0f6fab8ce0 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -127,7 +127,6 @@ def edam_formats( self, trans, **kwds ):
     def edam_data( self, trans, **kwds ):
         return self._datatypes_registry.edam_data
 
-
     @property
     def _datatypes_registry( self ):
         return self.app.datatypes_registry
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 74dbb21865e1..c6b19e2c3e74 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -112,7 +112,7 @@ def to_dict(x):
             "description": tool.description,
             "tool_id": tool.id,
             "inputs": input_param,
-            "outputs":output_param,
+            "outputs": output_param,
             "tool_version": tool.version,
             "section": tool.get_panel_section(),
             "dependency_shell_commands": tool.build_dependency_shell_commands(),
@@ -124,7 +124,6 @@ def to_dict(x):
             "guid": tool.guid,
         }
 
-
     @expose_api_anonymous
     def build( self, trans, id, **kwd ):
         """