diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index babdcb84fe2..07837255dc2 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -71,9 +71,8 @@ class ToolTestBuilder( object ):
# No explicit value for param in test case, determine from default
query_value = test_param.checked
else:
- # Test case supplied value, check cases against this.
- query_value = string_as_bool( declared_value )
- matches_declared_value = lambda case_value: string_as_bool(case_value) == query_value
+ query_value = _process_bool_param_value( test_param, declared_value )
+ matches_declared_value = lambda case_value: _process_bool_param_value( test_param, case_value ) == query_value
elif isinstance(test_param, galaxy.tools.parameters.basic.SelectToolParameter):
if declared_value is not None:
# Test case supplied explicit value to check against.
@@ -166,7 +165,8 @@ class ToolTestBuilder( object ):
# as a new instance with value defined and hence enter
# an infinite loop - hence the "case_value is not None"
# check.
- expanded_inputs[ case_context.for_state() ] = expanded_case_value
+ processed_value = _process_simple_value( value.test_param, expanded_case_value )
+ expanded_inputs[ case_context.for_state() ] = processed_value
elif isinstance( value, galaxy.tools.parameters.grouping.Section ):
context = ParamContext( name=value.name, parent_context=parent_context )
for r_name, r_value in value.inputs.iteritems():
@@ -203,33 +203,8 @@ class ToolTestBuilder( object ):
for ( name, value, extra ) in collection_def.collect_inputs():
require_file( name, value, extra, self.required_files )
processed_value = collection_def
- elif isinstance( value, galaxy.tools.parameters.basic.SelectToolParameter ) and hasattr( value, 'static_options' ):
- # Tests may specify values as either raw value or the value
- # as they appear in the list - the API doesn't and shouldn't
- # accept the text value - so we need to convert the text
- # into the form value.
- def process_param_value( param_value ):
- found_value = False
- value_for_text = None
- if value.static_options:
- for (text, opt_value, selected) in value.static_options:
- if param_value == opt_value:
- found_value = True
- if value_for_text is None and param_value == text:
- value_for_text = opt_value
- if not found_value and value_for_text is not None:
- processed_value = value_for_text
- else:
- processed_value = param_value
- return processed_value
- # Do replacement described above for lists or singleton
- # values.
- if isinstance( param_value, list ):
- processed_value = map( process_param_value, param_value )
- else:
- processed_value = process_param_value( param_value )
else:
- processed_value = param_value
+ processed_value = _process_simple_value( value, param_value )
expanded_inputs[ context.for_state() ] = processed_value
return expanded_inputs
@@ -240,6 +215,54 @@ class ToolTestBuilder( object ):
return require_file( name, value, extra, self.required_files )
+def _process_simple_value( param, param_value ):
+ if isinstance( param, galaxy.tools.parameters.basic.SelectToolParameter ) and hasattr( param, 'static_options' ):
+ # Tests may specify values as either raw value or the value
+ # as they appear in the list - the API doesn't and shouldn't
+ # accept the text value - so we need to convert the text
+ # into the form value.
+ def process_param_value( param_value ):
+ found_value = False
+ value_for_text = None
+ if param.static_options:
+ for (text, opt_value, selected) in param.static_options:
+ if param_value == opt_value:
+ found_value = True
+ if value_for_text is None and param_value == text:
+ value_for_text = opt_value
+ if not found_value and value_for_text is not None:
+ processed_value = value_for_text
+ else:
+ processed_value = param_value
+ return processed_value
+ # Do replacement described above for lists or singleton
+ # values.
+ if isinstance( param_value, list ):
+ processed_value = map( process_param_value, param_value )
+ else:
+ processed_value = process_param_value( param_value )
+ elif isinstance( param, galaxy.tools.parameters.basic.BooleanToolParameter ):
+ # Like above, tests may use the tool define values of simply
+ # true/false.
+ processed_value = _process_bool_param_value( param, param_value )
+ else:
+ processed_value = param_value
+ return processed_value
+
+
+def _process_bool_param_value( param, param_value ):
+ assert isinstance( param, galaxy.tools.parameters.basic.BooleanToolParameter )
+ if isinstance( param_value, list ):
+ param_value = param_value[0]
+ if param.truevalue == param_value:
+ processed_value = True
+ elif param.falsevalue == param_value:
+ processed_value = False
+ else:
+ processed_value = string_as_bool( param_value )
+ return processed_value
+
+
@nottest
def test_data_iter( required_files ):
for fname, extra in required_files:
diff --git a/test/functional/tools/boolean_conditional.xml b/test/functional/tools/boolean_conditional.xml
new file mode 100644
index 00000000000..df699e267a8
--- /dev/null
+++ b/test/functional/tools/boolean_conditional.xml
@@ -0,0 +1,53 @@
+
+
+ echo "$p1.p1val" >> $out_file1;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index deabd1d0062..68c81052ee7 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -3,6 +3,7 @@
+
diff --git a/test/functional/tools/simple_constructs.xml b/test/functional/tools/simple_constructs.xml
index d67c0c282ee..6fdde0ff154 100644
--- a/test/functional/tools/simple_constructs.xml
+++ b/test/functional/tools/simple_constructs.xml
@@ -61,5 +61,17 @@
+
+
+
+
+
+
+
diff --git a/tool-data/shared/gbrowse/gbrowse_build_sites.txt b/tool-data/shared/gbrowse/gbrowse_build_sites.txt
index 289af693b69..df21421f090 100644
--- a/tool-data/shared/gbrowse/gbrowse_build_sites.txt
+++ b/tool-data/shared/gbrowse/gbrowse_build_sites.txt
@@ -18,7 +18,7 @@ wormbase_ws225 WormBase WS225 http://ws225.wormbase.org/db/gb2/gbrowse/ caeAng1,
tair tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis,Arabidopsis_thaliana_TAIR10 arabidopsis_tair8,arabidopsis_tair9,arabidopsis
#modENCODE
-modencode modENCODE http://modencode.oicr.on.ca/fgb2/gbrowse/ ce6,dm2 worm,fly
+modencode modENCODE http://gbrowse.modencode.org/fgb2/gbrowse/ ce10,dm3 worm,fly
#Saccharomyces Genome Database (SGD)
sgd_yeast Saccharomyces Genome Database http://browse.yeastgenome.org/fgb2/gbrowse/ Saccharomyces_cerevisiae_S288C_SGD2010 scgenome
diff --git a/tools/data_source/fly_modencode.xml b/tools/data_source/fly_modencode.xml
index 7b14302ebec..3d3f5b8e533 100644
--- a/tools/data_source/fly_modencode.xml
+++ b/tools/data_source/fly_modencode.xml
@@ -1,21 +1,21 @@
-
+
server
data_source.py $output $__app__.config.output_size_limit
-
+
go to modENCODE fly server $GALAXY_URL
-
+
-
+
-
+
diff --git a/tools/data_source/worm_modencode.xml b/tools/data_source/worm_modencode.xml
index 074792cccf7..b021f4a0ddf 100644
--- a/tools/data_source/worm_modencode.xml
+++ b/tools/data_source/worm_modencode.xml
@@ -1,21 +1,21 @@
-
+
server
data_source.py $output $__app__.config.output_size_limit
-
+
go to modENCODE worm server $GALAXY_URL
-
+
-
+
-
+