Merge pull request #1 from jmchilton/tool_form_section_tag

Tool testing sections.

Author: guerler

lib/galaxy/tools/parser/xml.py

@@ -418,6 +418,13 @@ def __expand_input_elems( root_elem, prefix="" ):
         __pull_up_params( root_elem, cond_elem )
         root_elem.remove( cond_elem )
 
+    section_elems = root_elem.findall( 'section' )
+    for section_elem in section_elems:
+        new_prefix = __prefix_join( prefix, section_elem.get( "name" ) )
+        __expand_input_elems( section_elem, new_prefix )
+        __pull_up_params( root_elem, section_elem )
+        root_elem.remove( section_elem )
+
 
 def __append_prefix_to_params( elem, prefix ):
     for param_elem in elem.findall( 'param' ):

lib/galaxy/tools/test.py

@@ -166,7 +166,12 @@ def __process_raw_inputs( self, tool_inputs, raw_inputs, parent_context=None ):
                         # an infinite loop - hence the "case_value is not None"
                         # check.
                         expanded_inputs[ case_context.for_state() ] = expanded_case_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():
+                    expanded_input = self.__process_raw_inputs( { context.for_state(): r_value }, raw_inputs, parent_context=context )
+                    if expanded_input:
+                        expanded_inputs.update( expanded_input )
             elif isinstance( value, galaxy.tools.parameters.grouping.Repeat ):
                 repeat_index = 0
                 while True:
@@ -364,6 +369,13 @@ def expand_input_elems( root_elem, prefix="" ):
         __pull_up_params( root_elem, cond_elem )
         root_elem.remove( cond_elem )
 
+    section_elems = root_elem.findall( 'section' )
+    for section_elem in section_elems:
+        new_prefix = __prefix_join( prefix, section_elem.get( "name" ) )
+        expand_input_elems( section_elem, new_prefix )
+        __pull_up_params( root_elem, section_elem )
+        root_elem.remove( section_elem )
+
 
 def __append_prefix_to_params( elem, prefix ):
     for param_elem in elem.findall( 'param' ):

test/functional/tools/samples_tool_conf.xml

@@ -28,6 +28,7 @@
   <tool file="column_param.xml" />
   <tool file="column_multi_param.xml" />
   <tool file="special_params.xml" />
+  <tool file="section.xml" />
   <tool file="top_level_data.xml" />
   <tool file="validation_default.xml" />
   <tool file="validation_sanitizer.xml" />

test/functional/tools/section.xml

@@ -0,0 +1,43 @@
+<tool id="section" name="section">
+    <command>
+        echo "$int.inttest"   >> $out_file1; 
+        echo "$float.floattest" >> $out_file1; 
+    </command>
+    <inputs>
+        <section name="int" title="Integer Section" expanded="true">
+            <param name="inttest" value="1" type="integer" />
+        </section>
+        <section name="float" title="Float Section" expanded="false">
+            <param name="floattest" value="1.0" type="float" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inttest" value="12456" />
+            <param name="floattest" value="6.789" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="12456" />
+                    <has_line line="6.789" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <section name="int">
+                <param name="inttest" value="12456" />
+            </section>
+            <section name="float">
+                <param name="floattest" value="6.789" />
+            </section>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="12456" />
+                    <has_line line="6.789" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>