diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 8c12d282533..d80b279f87b 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -641,11 +641,22 @@ class Tool( object, Dictifiable ):
         root = tool_source.root
         conf_parent_elem = root.find("configfiles")
         if conf_parent_elem is not None:
+            inputs_elem = conf_parent_elem.find( "inputs" )
+            if inputs_elem is not None:
+                name = inputs_elem.get( "name" )
+                filename = inputs_elem.get( "filename", None )
+                format = inputs_elem.get("format", "json")
+                version_str = inputs_elem.get("version", "1")
+                if not version_str:
+                    raise ValueError("inputs configfile tag must define a version attribute")
+                version = int(version_str)
+                content = dict(format=format, version=version)
+                self.config_files.append( ( name, filename, content ) )
             for conf_elem in conf_parent_elem.findall( "configfile" ):
                 name = conf_elem.get( "name" )
                 filename = conf_elem.get( "filename", None )
-                text = conf_elem.text
-                self.config_files.append( ( name, filename, text ) )
+                content = conf_elem.text
+                self.config_files.append( ( name, filename, content ) )
 
     def __parse_trackster_conf(self, tool_source):
         self.trackster_conf = None
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 72da979a5d9..7f13c1a7df1 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -1,3 +1,4 @@
+import json
 import os
 import tempfile
 
@@ -20,6 +21,7 @@ from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
     SelectToolParameter,
 )
+from galaxy.tools.parameters import wrapped_json
 from galaxy.tools.parameters.grouping import Conditional, Repeat, Section
 from galaxy.tools import global_tool_errors
 from galaxy.jobs.datasets import dataset_path_rewrites
@@ -472,7 +474,8 @@ class ToolEvaluator( object ):
         """
         param_dict = self.param_dict
         config_filenames = []
-        for name, filename, template_text in self.tool.config_files:
+        for name, filename, content in self.tool.config_files:
+            config_text, is_template = self.__build_config_file_text(content)
             # If a particular filename was forced by the config use it
             directory = self.local_working_directory
             if filename is not None:
@@ -480,7 +483,7 @@ class ToolEvaluator( object ):
             else:
                 fd, config_filename = tempfile.mkstemp( dir=directory )
                 os.close( fd )
-            self.__write_workdir_file( config_filename, template_text, param_dict )
+            self.__write_workdir_file( config_filename, config_text, param_dict, is_template=is_template )
             self.__register_extra_file( name, config_filename )
             config_filenames.append( config_filename )
         return config_filenames
@@ -526,8 +529,20 @@ class ToolEvaluator( object ):
         else:
             return None
 
-    def __write_workdir_file( self, config_filename, template, context ):
-        value = fill_template( template, context=context )
+    def __build_config_file_text( self, content ):
+        if isinstance( content, basestring ):
+            return content, True
+
+        assert content["format"] == "json"
+        assert content["version"] == 1
+
+        return json.dumps(wrapped_json.json_wrap(self.tool.inputs, self.param_dict)), False
+
+    def __write_workdir_file( self, config_filename, content, context, is_template=True ):
+        if is_template:
+            value = fill_template( content, context=context )
+        else:
+            value = content
         with open( config_filename, "w" ) as f:
             f.write( value )
         # For running jobs as the actual user, ensure the config file is globally readable
diff --git a/lib/galaxy/tools/parameters/wrapped_json.py b/lib/galaxy/tools/parameters/wrapped_json.py
new file mode 100644
index 00000000000..e49cee48622
--- /dev/null
+++ b/lib/galaxy/tools/parameters/wrapped_json.py
@@ -0,0 +1,72 @@
+import logging
+log = logging.getLogger(__name__)
+
+
+def json_wrap(inputs, input_values, as_dict=None, handle_files="SKIP"):
+    if as_dict is None:
+        as_dict = {}
+
+    for input in inputs.itervalues():
+        input_name = input.name
+        input_type = input.type
+        value = input_values[input_name]
+        if input_type == "repeat":
+            repeat_job_value = []
+            for d in input_values[input.name]:
+                repeat_instance_job_value = {}
+                json_wrap(input.inputs, d, repeat_instance_job_value)
+                repeat_job_value.append(repeat_instance_job_value)
+            as_dict[input_name] = repeat_job_value
+        if input_type == "conditional":
+            values = input_values[input_name]
+            current = values["__current_case__"]
+            conditional_job_value = {}
+            json_wrap(input.cases[current].inputs, values, conditional_job_value)
+            as_dict[input_name] = conditional_job_value
+        if input_type == "section":
+            values = input_values[input_name]
+            section_job_value = {}
+            json_wrap(input.inputs, values, section_job_value)
+            as_dict[input_name] = section_job_value
+        elif input_type == "data" and input.multiple:
+            if handle_files == "SKIP":
+                continue
+            raise NotImplementedError()
+        elif input_type == "data":
+            if handle_files == "SKIP":
+                continue
+            raise NotImplementedError()
+        elif input_type == "data_collection":
+            if handle_files == "SKIP":
+                continue
+            raise NotImplementedError()
+        elif input_type == "select" or input_type == "text":
+            value = input_values[input_name]
+            json_value = _cast_if_not_none(value, str)
+            as_dict[input_name] = json_value
+        elif input_type == "float":
+            value = input_values[input_name]
+            json_value = _cast_if_not_none(value, float, empty_to_none=True)
+            as_dict[input_name] = json_value
+        elif input_type == "integer":
+            value = input_values[input_name]
+            json_value = _cast_if_not_none(value, int, empty_to_none=True)
+            as_dict[input_name] = json_value
+        elif input_type == "boolean":
+            value = input_values[input_name]
+            json_value = _cast_if_not_none(value, bool)
+            as_dict[input_name] = json_value
+        else:
+            raise NotImplementedError("input_type [%s] not implemented" % input_type)
+    return as_dict
+
+
+def _cast_if_not_none(value, cast_to, empty_to_none=False):
+    # log.debug("value [%s], type[%s]" % (value, type(value)))
+    if value is None or (empty_to_none and str(value) == ''):
+        return None
+    else:
+        return cast_to(value)
+
+
+__all__ = ['json_wrap']
diff --git a/test/functional/tools/inputs_as_json.xml b/test/functional/tools/inputs_as_json.xml
new file mode 100644
index 00000000000..a4f5a4de91c
--- /dev/null
+++ b/test/functional/tools/inputs_as_json.xml
@@ -0,0 +1,79 @@
+<tool id="inputs_as_json" name="inputs_as_json" version="1.0.0">
+    <configfiles>
+        <inputs name="inputs" format="json" version="1" />
+        <configfile name="check_inputs"><![CDATA[
+import json
+import sys
+
+input_json_path = sys.argv[1]
+test_case = sys.argv[2]
+as_dict = json.load(open(input_json_path, "r"))
+
+
+def assert_equals(x, y):
+    assert x == y, "%s != %s" % (x, y)
+
+if test_case == "1":
+    assert_equals(as_dict["test_case"], 1)
+    assert_equals(as_dict["text_test"], "foo")
+    assert_equals(as_dict["booltest"], True)
+    assert_equals(as_dict["inttest"], 12456)
+    assert_equals(as_dict["floattest"], 6.789)
+    assert_equals(as_dict["radio_select"], "a_radio")
+elif test_case == "2":
+    assert_equals(as_dict["test_case"], 2)
+    assert_equals(as_dict["text_test"], "bar")
+    assert_equals(as_dict["booltest"], False)
+    assert_equals(as_dict["inttest"], None)
+    assert_equals(as_dict["floattest"], 1.0)
+    assert_equals(as_dict["radio_select"], "a_radio")
+
+with open("output", "w") as f:
+    f.write("okay\n")
+]]></configfile>
+    </configfiles>
+    <command>
+        python $check_inputs $inputs $test_case
+    </command>
+    <inputs>
+        <param name="test_case" type="integer" value="0" />
+        <param name="text_test" type="text" />
+        <param name="booltest" truevalue="booltrue" falsevalue="boolfalse" checked="false" type="boolean" />
+        <param name="inttest" type="integer" optional="true" />
+        <param name="floattest" value="1.0" type="float" />
+        <param name="radio_select" type="select" display="radio">
+            <option value="a_radio" selected="true">A Radio</option>
+            <option value="b_radio">B Radio</option>
+            <option value="c_radio">C Radio</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file1" from_work_dir="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="test_case" value="1" />
+            <param name="text_test" value="foo" />
+            <param name="booltest" value="true" />
+            <param name="inttest" value="12456" />
+            <param name="floattest" value="6.789" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="okay" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="test_case" value="2" />
+            <param name="text_test" value="bar" />
+            <param name="booltest" value="false" />
+            <!-- Testing null integers -->
+            <!-- <param name="inttest" value="12456" /> -->
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="okay" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 509a37c78ae..3d7be1d164b 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -15,6 +15,7 @@
   <tool file="multi_output.xml" />
   <tool file="multi_output_configured.xml" />
   <tool file="multi_output_assign_primary.xml" />
+  <tool file="inputs_as_json.xml" />
   <tool file="dbkey_filter_input.xml" />
   <tool file="dbkey_filter_multi_input.xml" />
   <tool file="composite_output.xml" />