Implement special config file to dump parameters as json.

```
    <configfiles>
        <inputs name="inputs" format="json" version="1" />
    </configfiles>
```

Version is specified as 1, because the Galaxy tool plumbing doesn't really distinguish between parameter is '', parameter was explicitly supplied as None, parameter was absent, etc... - everything is a just a string in some ways. This distinction may be more important with JSON and for instance the CWL will require more percision, so we may want to revise Galaxy's tool handling in a backward compatible way someday.

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

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

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']

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>

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" />