From 43d2cb311d875298574a4dec56b7c1641ca8dc3b Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Wed, 16 Apr 2008 18:33:26 +0000 Subject: [PATCH] Fix for optional DataToolParameters and fix for GMAJ tool imports. --- lib/galaxy/tools/parameters/basic.py | 8 ++++++-- tools/visualization/GMAJ.py | 1 + 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 9ede8007434..71b8d9c057c 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -748,6 +748,7 @@ class DataToolParameter( ToolParameter ): formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) self.formats = tuple( formats ) self.multiple = str_bool( elem.get( 'multiple', False ) ) + # Optional DataToolParameters are used in tools like GMAJ and LAJ self.optional = str_bool( elem.get( 'optional', False ) ) #TODO: Enhance dynamic options for DataToolParameters #Currently, only the special case key='build' of type='data_meta' is a valid filter @@ -789,8 +790,11 @@ class DataToolParameter( ToolParameter ): if value is None or len( field.options ) == 1: # Ensure that the last item is always selected a, b, c = field.options[-1] - field.options[-1] = a, b, True - elif self.optional: + if self.optional: + field.options[-1] = a, b, False + else: + field.options[-1] = a, b, True + if self.optional: field.add_option( "Selection is Optional", 'None', True ) return field diff --git a/tools/visualization/GMAJ.py b/tools/visualization/GMAJ.py index 205e08ac6da..db0055daad8 100644 --- a/tools/visualization/GMAJ.py +++ b/tools/visualization/GMAJ.py @@ -4,6 +4,7 @@ Script that Creates a zip file for use by GMAJ """ import os, sys, zipfile +from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.align import maf