diff --git a/.travis.yml b/.travis.yml
index 335452a..c1743ab 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,6 @@
 language: python
 python:
-- '3.6'
+- '3.7'
 install: pip install -r requirements.txt
 script:
 - pip install -q -U setuptools
@@ -8,25 +8,37 @@ script:
 - pip install -q -U flake8
 - pip install -q -U xmldiff
 - pip install -q -r requirements.txt
-- python setup.py install
-- flake8 argparse2tool --ignore=E2,E3,E4,E5,W3,W505
-- PYTHONPATH=$(argparse2tool) python examples/example.py --generate_galaxy_xml > tmp.xml
+- python3 -m pip install --no-deps --no-cache-dir --force-reinstall .
+# temporarily install galaxyxml from branch https://github.com/hexylena/galaxyxml/pull/18
+- git clone -b topic/macros https://github.com/bernt-matthias/galaxyxml.git && cd galaxyxml && python3 -m pip install --no-deps --no-cache-dir --force-reinstall . && cd ..
+- flake8 argparse2tool --ignore=C901,E2,E3,E4,E5,W3,W505
+- PYTHONPATH=$(argparse2tool) python examples/example.py --generate_galaxy_xml -m examples/macros.xml > tmp.xml
 - xmldiff tmp.xml examples/example.xml
-- planemo lint --report_level all --fail_level error --xsd tmp.xml
+- planemo lint --skip tests --report_level all --fail_level error --xsd tmp.xml
 
 # Galaxy tool generation for example with subparsers -- generating one large (invalid) tool
 - echo '<root>' > tmp-sub.xml # wrap in extra level
-- PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml >> tmp-sub.xml
+- PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml -m examples/macros.xml >> tmp-sub.xml
 - echo '</root>' >> tmp-sub.xml
 - xmldiff tmp-sub.xml <(echo "<root>"; cat examples/example-sub.xml; echo "</root>")
 
-# Galaxy tool generation for example with subparsers -- generating separate tools
-- PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml --command foo > tmp-sub-foo.xml
-- PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml --command bar > tmp-sub-bar.xml
-- xmldiff tmp-sub-foo.xml examples/example-sub-foo.xml
-- planemo lint --report_level all --fail_level error --xsd tmp-sub-foo.xml
-- xmldiff tmp-sub-bar.xml examples/example-sub-bar.xml
-- planemo lint --report_level all --fail_level error --xsd tmp-sub-bar.xml
+# Galaxy tool generation for example with subparsers -- generating separate tools (this does not generate macro xml files automatically)
+- PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml -m examples/macros.xml --command foo > tmp-sub-foo.xml
+- PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml -m examples/macros.xml --command bar > tmp-sub-bar.xml
+- xmldiff tmp-sub-foo.xml examples/example-sub/example_sub_foo.xml
+- xmldiff tmp-sub-bar.xml examples/example-sub/example_sub_bar.xml
+
+# Galaxy tool generation for example with subparsers -- generating all tools and macros at once also include multiple macro files
+- mkdir tmp && cp examples/macros*xml tmp/
+- PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml -m examples/macros.xml -m examples/macros_tests.xml --directory tmp
+- ls tmp/
+- xmldiff tmp/example_sub_foo.xml examples/example-sub/example_sub_foo.xml
+- planemo lint --skip tests --report_level all --fail_level error --xsd  tmp/example_sub_foo.xml
+- xmldiff tmp/example_sub_bar.xml examples/example-sub/example_sub_bar.xml
+- planemo lint --skip tests --report_level all --fail_level error --xsd  tmp/example_sub_bar.xml
+- xmldiff tmp/example_sub_baz.xml examples/example-sub/example_sub_baz.xml
+- xmldiff tmp/example_sub_qux.xml examples/example-sub/example_sub_qux.xml
+
 
 - PYTHONPATH=$(argparse2tool) python examples/example.py --generate_cwl_tool > tmp.cwl
 - PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_cwl_tool > tmp-sub.cwl
@@ -37,7 +49,6 @@ script:
 - diff tmp-click.cwl examples/example-click.cwl
 before_deploy:
 - sed -i "s/__version__.*/__version__= '${TRAVIS_TAG}'/g" argparse2tool/__init__.py
-deploy:
 deploy:
   provider: pypi
   username: __token__
diff --git a/argparse2tool/__init__.py b/argparse2tool/__init__.py
index f87bc88..0245d43 100644
--- a/argparse2tool/__init__.py
+++ b/argparse2tool/__init__.py
@@ -48,3 +48,11 @@ def load_conflicting_package(name, not_name, module_number):
             imp.load_module(random_name, f, pathname, desc)
             return sys.modules[random_name]
     return None
+
+
+def remove_extension(name):
+    if name is not None:
+        name = name.replace('.py', '')
+        name = name.replace('-', '_')
+        name = name.replace(' ', '_')
+    return name
diff --git a/argparse2tool/cmdline2gxml/__init__.py b/argparse2tool/cmdline2gxml/__init__.py
index 81a0e9d..050157a 100644
--- a/argparse2tool/cmdline2gxml/__init__.py
+++ b/argparse2tool/cmdline2gxml/__init__.py
@@ -23,5 +23,9 @@ def __init__(self):
 
     def process_arguments(self):
         self.parser.add_argument('--generate_galaxy_xml', action='store_true')
+        self.parser.add_argument('-d', '--directory',
+                                 help='Directory to store tool descriptions')
+        self.parser.add_argument('-m', '--macro', action="append",
+                                 help='A global macro file to include in all tools')
         self.parser.add_argument('--command', action='store', default="")
         return vars(self.parser.parse_args())
diff --git a/argparse2tool/dropins/argparse/__init__.py b/argparse2tool/dropins/argparse/__init__.py
index 616267a..9f11d5e 100644
--- a/argparse2tool/dropins/argparse/__init__.py
+++ b/argparse2tool/dropins/argparse/__init__.py
@@ -1,6 +1,11 @@
+import os.path
 import re
+import shutil
 import sys
-from argparse2tool import load_argparse
+from argparse2tool import (
+    load_argparse,
+    remove_extension
+)
 from argparse2tool.cmdline2gxml import Arg2GxmlParser
 from argparse2tool.cmdline2cwl import Arg2CWLParser
 
@@ -21,6 +26,15 @@
     setattr(__selfmodule__, x, getattr(ap, x))
 
 tools = []
+# set of prog names where the argparser actually should be represented
+# as a macro, i.e. XYZ will be in the set if there is a
+# ArgumentParser(..., parents=[XYZ], ...)
+macros = set()
+
+# mapping tools to list of required macros (which are actually identical to the
+# parents parameter passed ArgumentParser. but I could not find out how this is
+# stored in the created ArgumentParser objects
+used_macros = dict()
 
 
 class ArgumentParser(ap.ArgumentParser):
@@ -37,10 +51,20 @@ def __init__(self,
                  argument_default=None,
                  conflict_handler='error',
                  add_help=True):
+        global macros
+        global used_macros
 
         self.argument_list = []
         self.argument_names = []
         tools.append(self)
+        if len(parents) > 0:
+            p = set([remove_extension(_.prog) for _ in parents])
+            macros = macros.union(p)
+            used_macros[remove_extension(prog)] = p
+
+        if '--generate_galaxy_xml' in sys.argv:
+            parents = []
+
         super(ArgumentParser, self).__init__(prog=prog,
                                              usage=usage,
                                              description=description,
@@ -109,6 +133,8 @@ def parse_args_cwl(self, *args, **kwargs):
                                 tool.inputs.append(cwlt_parameter)
                                 if isinstance(cwlt_parameter, cwlt.OutputParam):
                                     tool.outputs.append(cwlt_parameter)
+                        else:
+                            print("%s not implemented (%s)" % (argument_type, result.option_strings), file=sys.stderr)
 
                     if argp.epilog is not None:
                         tool.description += argp.epilog
@@ -128,6 +154,31 @@ def parse_args_cwl(self, *args, **kwargs):
         sys.exit(0)
 
     def parse_args_galaxy(self, *args, **kwargs):
+        global used_macros
+
+        directory = kwargs.get('directory', None)
+        macro = kwargs.get('macro', None)
+
+        # copy macros to destination dir
+        if directory and macro:
+            for i, m in enumerate(macro):
+                macro[i] = os.path.basename(m)
+                shutil.copyfile(m, os.path.join(directory, macro[i]))
+
+        # since macros can also make use of macros (i.e. the parent relation
+        # specified in the arguments can be nester) we need to extend the
+        # used macros such that really all are included
+        ext_used_macros = dict()
+        for tool, macros in used_macros.items():
+            ext_used_macros[tool] = set()
+            q = list(macros)
+            while len(q) > 0:
+                m = q.pop()
+                if m in used_macros:
+                    q.extend(used_macros[m])
+                ext_used_macros[tool].add(m)
+        used_macros = ext_used_macros
+
         for argp in tools:
             # make subparser description out of its help message
             if argp._subparsers:
@@ -139,53 +190,119 @@ def parse_args_galaxy(self, *args, **kwargs):
                         subparser.choices[choice_action.dest].description = choice_action.help
             else:
                 if kwargs.get('command', argp.prog) in argp.prog:
-                    data = self._parse_args_galaxy_argp(argp)
-                    print(data)
+                    data = self._parse_args_galaxy_argp(argp, macro)
+                    if directory:
+                        if directory[-1] != '/':
+                            directory += '/'
+                        filename = remove_extension(argp.prog) + ".xml"
+                        filename = directory + filename
+                        with open(filename, 'w') as f:
+                            f.write(data)
+                    else:
+                        print(data)
                 else:
                     continue
         sys.exit(0)
 
-    def _parse_args_galaxy_argp(self, argp):
+    def _parse_args_galaxy_argp(self, argp, macro):
+        global macros
+        global used_macros
+
         try:
             version = self.print_version() or '1.0'
         except AttributeError:  # handle the potential absence of print_version
             version = '1.0'
-        tool = gxt.Tool(argp.prog,
-                        argp.prog.replace(" ", "_"),
-                        version,
-                        argp.description,
-                        "python "+argp.prog,
-                        interpreter=None,
-                        version_command='python %s --version' % argp.prog)
+        print("_parse_args_galaxy_argp _subparsers %s" % argp._subparsers)
+        prog = remove_extension(argp.prog)
 
-        inputs = gxtp.Inputs()
-        outputs = gxtp.Outputs()
+        # tid = argp.prog.split()[-1]
+
+        # get the list of file names of the used macros
+        mx = used_macros.get(prog, [])
+        mx = sorted(["%s.xml" % _.split(" ")[-1] for _ in mx])
+
+        if prog not in macros:
+            tpe = gxt.Tool
+            if macro:
+                mx.extend(macro)
+        else:
+            tpe = gxt.MacrosTool
+
+        tool = tpe(prog,
+                   prog.replace(" ", "_"),
+                   version,
+                   argp.description,
+                   "python "+argp.prog,
+                   interpreter=None,
+                   version_command='python %s --version' % argp.prog,
+                   macros=mx)
+
+        inputs = tool.inputs
+        outputs = tool.outputs
+        sections = dict()
 
         at = agt.ArgparseGalaxyTranslation()
-        # Only build up arguments if the user actually requests it
-        for result in argp.argument_list:
+
+        for group in argp._action_groups:
+            if group in [argp._positionals, argp._optionals]:
+                continue
+            argument_type = group.__class__.__name__
+            methodToCall = getattr(at, argument_type)
+            sections[group] = methodToCall(group, tool=tool)
+
+        for action in argp._actions:
             # I am SO thankful they return the argument here. SO useful.
-            argument_type = result.__class__.__name__
+            argument_type = action.__class__.__name__
             # http://stackoverflow.com/a/3071
             if hasattr(at, argument_type):
                 methodToCall = getattr(at, argument_type)
-                gxt_parameter = methodToCall(result, tool=tool)
-                if gxt_parameter is not None:
-                    if isinstance(gxt_parameter, gxtp.InputParameter):
-                        inputs.append(gxt_parameter)
-                    else:
-                        outputs.append(gxt_parameter)
+                gxt_parameter = methodToCall(action, tool=tool)
+                ## print(action, gxt_parameter)
+                print(action.option_strings, action.container)
+                if gxt_parameter is None:  # e.g. for help and version actions
+                    continue
+                if not isinstance(gxt_parameter, gxtp.InputParameter):
+                    outputs.append(gxt_parameter)
+                elif action.container in sections:
+                    sections[action.container].append(gxt_parameter)
+                else:
+                    inputs.append(gxt_parameter)
+            else:
+                print("%s not implemented (%s)" % (argument_type, action.option_strings), file=sys.stderr)
+
+        for section in sections:
+            inputs.append(sections[section])
+
 
-        # TODO: replace with argparse-esque library to do this.
-        stdout = gxtp.OutputData('default', 'txt')
-        stdout.command_line_override = '> $default'
-        outputs.append(stdout)
+#         print("argp._action_groups %s" % argp._action_groups)
+#         # Only build up arguments if the user actually requests it
+#         for result in argp.argument_list:
+#             # I am SO thankful they return the argument here. SO useful.
+#             argument_type = result.__class__.__name__
+#             print("_parse_args_galaxy_argp %s type %s [%s]" % (getattr(result, "title", "no title"), argument_type, hasattr(at, argument_type)))
+#             # http://stackoverflow.com/a/3071
+#             if hasattr(at, argument_type):
+#                 methodToCall = getattr(at, argument_type)
+#                 gxt_parameter = methodToCall(result, tool=tool)
+#                 if gxt_parameter is not None:
+#                     if isinstance(gxt_parameter, gxtp.InputParameter):
+#                         inputs.append(gxt_parameter)
+#                     else:
+#                         outputs.append(gxt_parameter)
+
+        if prog in used_macros:
+            for m in sorted(used_macros[prog]):
+                inputs.append(gxtp.ExpandIO(m + "_inmacro"))
+                outputs.append(gxtp.ExpandIO(m + "_outmacro"))
+
+        if prog not in macros:
+            # TODO: replace with argparse-esque library to do this.
+            stdout = gxtp.OutputData('default', 'txt')
+            stdout.command_line_override = '> $default'
+            outputs.append(stdout)
 
-        tool.inputs = inputs
-        tool.outputs = outputs
         if argp.epilog is not None:
             tool.help = argp.epilog
         else:
             tool.help = "TODO: Write help"
-
         return tool.export()
diff --git a/argparse2tool/dropins/argparse/argparse_cwl_translation.py b/argparse2tool/dropins/argparse/argparse_cwl_translation.py
index 11950f6..9fa4dbc 100644
--- a/argparse2tool/dropins/argparse/argparse_cwl_translation.py
+++ b/argparse2tool/dropins/argparse/argparse_cwl_translation.py
@@ -77,6 +77,12 @@ def __args_from_nargs(self, param):
 
         return param
 
+    def _VersionAction(self, param, tool=None):
+        pass
+
+    def _HelpAction(self, param, tool=None):
+        pass
+
     def _StoreAction(self, param):
         param = self.__args_from_nargs(param)
         cwlparam = self.__cwl_param_from_type(param)
@@ -110,6 +116,11 @@ def __StoreBoolAction(self, param):
         cwlparam = self.__cwl_param_from_type(param)
         return cwlparam
 
+    def _StoreConstAction(self, param):
+        param.type = bool
+        cwlparam = self.__cwl_param_from_type(param)
+        return cwlparam
+
     @staticmethod
     def get_cwl_type(py_type):
         """
diff --git a/argparse2tool/dropins/argparse/argparse_galaxy_translation.py b/argparse2tool/dropins/argparse/argparse_galaxy_translation.py
index 7898967..2345108 100644
--- a/argparse2tool/dropins/argparse/argparse_galaxy_translation.py
+++ b/argparse2tool/dropins/argparse/argparse_galaxy_translation.py
@@ -1,7 +1,7 @@
-import galaxyxml.tool.parameters as gxtp
 from collections import Counter
 from pydoc import locate
 
+import galaxyxml.tool.parameters as gxtp
 
 class ArgparseGalaxyTranslation(object):
 
@@ -30,7 +30,7 @@ def __gxtp_param_from_type(self, param, flag, label, num_dashes, gxparam_extra_k
             gxparam = gxtp.DataParam(flag, label=label, num_dashes=num_dashes, **gxparam_extra_kwargs)
         elif isinstance(param.type, FileType):
             if 'w' in param.type._mode:
-                gxparam = gxtp.OutputParameter(
+                gxparam = gxtp.OutputData(
                     flag, format='data', default=default, label=label,
                     num_dashes=num_dashes, **gxparam_extra_kwargs
                 )
@@ -119,7 +119,7 @@ def __args_from_nargs(self, param, repeat_name, repeat_var_name, positional, fla
             gxrepeat_cli_after = ''
             gxrepeat_cli_before = """\n#set %s = '" "'.join([ str($var.%s) for $var in $%s ])""" % (repeat_var_name, flag, repeat_name)
         else:
-            raise Exception("TODO: Handle argparse.REMAINDER")
+            raise Exception("Unknown nargs value %s" % param.nargs)
 
         return (gxrepeat_args, gxrepeat_kwargs, gxrepeat_cli_after,
                 gxrepeat_cli_before, gxrepeat_cli_actual, gxparam_cli_before, gxparam_cli_after)
@@ -138,6 +138,9 @@ def _VersionAction(self, param, tool=None):
         # Count the repeats for unique names
         # TODO improve
 
+    def _HelpAction(self, param, tool=None):
+        pass
+
     def _StoreAction(self, param, tool=None):
         """
         Parse argparse arguments action type of "store", the default.
@@ -148,7 +151,6 @@ def _StoreAction(self, param, tool=None):
         gxrepeat = None
         self.repeat_count += 1
         gxparam_extra_kwargs = {}
-
         if not param.required:
             gxparam_extra_kwargs['optional'] = True
 
@@ -247,3 +249,8 @@ def _StoreConstAction(self, param, **kwargs):
         gxparam = gxtp.BooleanParam(flag_wo_dashes, label=param.help, num_dashes=num_dashes)
 
         return gxparam
+
+    def _ArgumentGroup(self, param, **kwargs):
+        return gxtp.Section(name= param.title.replace(" ", "_"),
+                            title=param.title,
+                            help=param.description)
diff --git a/examples/example-sub.cwl b/examples/example-sub.cwl
index db95e46..fcd0d41 100644
--- a/examples/example-sub.cwl
+++ b/examples/example-sub.cwl
@@ -1,5 +1,73 @@
 #!/usr/bin/env cwl-runner
-# This tool description was generated automatically by argparse2tool
+# This tool description was generated automatically by argparse2tool ver. 0.4.9
+# To generate again: $ example-sub.py --generate_cwl_tool
+# Help: $ example --help_arg2cwl
+
+cwlVersion: v1.0
+
+class: CommandLineTool
+baseCommand: ['example-sub.py', 'qux']
+
+doc: |
+  None
+
+inputs:
+  
+  qux:
+    type:
+    - "null"
+    - type: array
+      items: string
+
+    doc: qux help
+    inputBinding:
+      prefix: --qux 
+
+
+outputs:
+    []
+
+#!/usr/bin/env cwl-runner
+# This tool description was generated automatically by argparse2tool ver. 0.4.9
+# To generate again: $ example-sub.py --generate_cwl_tool
+# Help: $ example --help_arg2cwl
+
+cwlVersion: v1.0
+
+class: CommandLineTool
+baseCommand: ['example-sub.py', 'baz']
+
+doc: |
+  None
+
+inputs:
+  
+  qux:
+    type:
+    - "null"
+    - type: array
+      items: array
+
+    doc: qux help
+    inputBinding:
+      prefix: --qux 
+
+  baz:
+    type:
+    - "null"
+    - type: array
+      items: string
+
+    doc: baz help
+    inputBinding:
+      prefix: --baz 
+
+
+outputs:
+    []
+
+#!/usr/bin/env cwl-runner
+# This tool description was generated automatically by argparse2tool ver. 0.4.9
 # To generate again: $ example-sub.py --generate_cwl_tool
 # Help: $ example --help_arg2cwl
 
@@ -13,6 +81,26 @@ doc: |
 
 inputs:
   
+  qux:
+    type:
+    - "null"
+    - type: array
+      items: array
+
+    doc: qux help
+    inputBinding:
+      prefix: --qux 
+
+  baz:
+    type:
+    - "null"
+    - type: array
+      items: array
+
+    doc: baz help
+    inputBinding:
+      prefix: --baz 
+
   keyword:
     type:
       type: array
@@ -31,6 +119,13 @@ inputs:
     inputBinding:
       position: 2
 
+  accumulate:
+    type: ["null", boolean]
+    default: <built-in function max>
+    doc: sum the integers (default - find the max)
+    inputBinding:
+      prefix: -s 
+
   foo:
     type: ["null", string]
     doc: foo help
@@ -60,7 +155,7 @@ outputs:
     []
 
 #!/usr/bin/env cwl-runner
-# This tool description was generated automatically by argparse2tool
+# This tool description was generated automatically by argparse2tool ver. 0.4.9
 # To generate again: $ example-sub.py --generate_cwl_tool
 # Help: $ example --help_arg2cwl
 
@@ -74,6 +169,16 @@ doc: |
 
 inputs:
   
+  qux:
+    type:
+    - "null"
+    - type: array
+      items: array
+
+    doc: qux help
+    inputBinding:
+      prefix: --qux 
+
   false:
     type: ["null", boolean]
     default: True
diff --git a/examples/example-sub.py b/examples/example-sub.py
index b5da603..51fdd5c 100644
--- a/examples/example-sub.py
+++ b/examples/example-sub.py
@@ -3,30 +3,31 @@
 
 parent = argparse.ArgumentParser(description='Process some integers.', prefix_chars='-+', epilog="here's some epilog text", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-
 subparsers = parent.add_subparsers()
 
-parser_foo = subparsers.add_parser('foo')
-parser_bar = subparsers.add_parser('bar')
+parser_qux = subparsers.add_parser('qux', add_help=False)
+parser_qux.add_argument('--qux', metavar='QUX', type=str, nargs=1, help='qux help')
 
-parser_foo.add_argument('keyword', metavar='Q', type=str, nargs=1, help='action keyword')
+parser_baz = subparsers.add_parser('baz', parents=[parser_qux], add_help=False)
+parser_baz.add_argument('--baz', metavar='BAZ', type=str, nargs=1, help='baz help')
 
+parser_foo = subparsers.add_parser('foo', parents=[parser_baz])
+parser_foo.add_argument('keyword', metavar='Q', type=str, nargs=1,
+                        help='action keyword')
 parser_foo.add_argument('integers', metavar='N', type=int, nargs='+',
-                    help='an integer for the accumulator')
-
+                        help='an integer for the accumulator')
 parser_foo.add_argument('--sum', '-s', dest='accumulate', action='store_const',
-                    const=sum, default=max, help='sum the integers (default: find the max)')
-
+                        const=sum, default=max,
+                        help='sum the integers (default: find the max)')
 parser_foo.add_argument('--foo', nargs='?', help='foo help')
 parser_foo.add_argument('--bar', nargs='*', default=[1, 2, 3], help='BAR!')
 parser_foo.add_argument('--true', action='store_true', help='Store a true')
+
+parser_bar = subparsers.add_parser('bar', parents=[parser_qux])
 parser_bar.add_argument('--false', action='store_false', help='Store a false')
 parser_bar.add_argument('--append', action='append', help='Append a value')
-
 parser_bar.add_argument('--nargs2', nargs=2, help='nargs2')
-
 parser_bar.add_argument('--mode', choices=['rock', 'paper', 'scissors'], default='scissors')
-
-
 parser_bar.add_argument('--version', action='version', version='2.0')
+
 args = parent.parse_args()
diff --git a/examples/example-sub.xml b/examples/example-sub.xml
index 56dae02..980580f 100644
--- a/examples/example-sub.xml
+++ b/examples/example-sub.xml
@@ -1,8 +1,35 @@
-<tool id="example-sub.py_foo" name="example-sub.py foo" version="1.0">
+<root>
+<macros>
+  <token name="EXAMPLE_SUB_QUX_INMACRO"><![CDATA[--qux '$qux']]></token>
+  <token name="EXAMPLE_SUB_QUX_OUTMACRO"><![CDATA[]]></token>
+  <xml name="example_sub_qux_inmacro">
+    <param optional="true" label="qux help" type="text" name="qux" argument="--qux"/>
+  </xml>
+  <xml name="example_sub_qux_outmacro"/>
+</macros>
+
+<macros>
+  <token name="EXAMPLE_SUB_BAZ_INMACRO"><![CDATA[--baz '$baz'
+@EXAMPLE_SUB_QUX_INMACRO@]]></token>
+  <token name="EXAMPLE_SUB_BAZ_OUTMACRO"><![CDATA[@EXAMPLE_SUB_QUX_OUTMACRO@]]></token>
+  <xml name="example_sub_baz_inmacro">
+    <param optional="true" label="baz help" type="text" name="baz" argument="--baz"/>
+    <expand macro="example_sub_qux_inmacro"/>
+  </xml>
+  <xml name="example_sub_baz_outmacro">
+    <expand macro="example_sub_qux_outmacro"/>
+  </xml>
+</macros>
+
+<tool name="example_sub_foo" id="example_sub_foo" version="1.0">
   <description/>
-  <stdio>
-    <exit_code level="fatal" range="1:"/>
-  </stdio>
+  <macros>
+    <import>example_sub_baz.xml</import>
+    <import>example_sub_qux.xml</import>
+    <import>examples/macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
   <version_command><![CDATA[python example-sub.py foo --version]]></version_command>
   <command><![CDATA[python example-sub.py foo $keyword
 
@@ -12,38 +39,51 @@
 $sum
 
 #if $foo and $foo is not None:
---foo $foo
+--foo '$foo'
 #end if
 
 #set repeat_var_4 = '" "'.join([ str($var.bar) for $var in $repeat_4 ])
 --bar "$repeat_var_4"
 
 $true
+@EXAMPLE_SUB_BAZ_INMACRO@
+@EXAMPLE_SUB_QUX_INMACRO@
+@EXAMPLE_SUB_BAZ_OUTMACRO@
+@EXAMPLE_SUB_QUX_OUTMACRO@
 > $default]]></command>
   <inputs>
-    <param label="action keyword" name="keyword" type="text"/>
-    <repeat min="1" name="repeat_2" title="repeat_title">
-      <param label="an integer for the accumulator" name="integers" type="integer" value="0"/>
+    <param label="action keyword" type="text" name="keyword"/>
+    <repeat title="repeat_title" min="1" name="repeat_2">
+      <param label="an integer for the accumulator" value="0" type="integer" name="integers"/>
     </repeat>
-    <param argument="--sum" checked="false" label="sum the integers (default: find the max)" name="sum" type="boolean" truevalue="--sum" falsevalue=""/>
-    <param argument="--foo" label="foo help" name="foo" optional="true" type="text"/>
-    <repeat name="repeat_4" title="repeat_title">
-      <param argument="--bar" label="BAR!" name="bar" optional="true" type="text" value="1"/>
+    <param label="sum the integers (default: find the max)" checked="false" type="boolean" name="sum" argument="--sum" truevalue="--sum" falsevalue=""/>
+    <param optional="true" label="foo help" type="text" name="foo" argument="--foo"/>
+    <repeat title="repeat_title" name="repeat_4">
+      <param optional="true" label="BAR!" value="1" type="text" name="bar" argument="--bar"/>
     </repeat>
-    <param argument="--true" checked="false" label="Store a true" name="true" type="boolean" truevalue="--true" falsevalue=""/>
+    <param label="Store a true" checked="false" type="boolean" name="true" argument="--true" truevalue="--true" falsevalue=""/>
+    <expand macro="example_sub_baz_inmacro"/>
+    <expand macro="example_sub_qux_inmacro"/>
   </inputs>
   <outputs>
-    <data format="txt" hidden="false" name="default"/>
+    <expand macro="example_sub_baz_outmacro"/>
+    <expand macro="example_sub_qux_outmacro"/>
+    <data name="default" format="txt" hidden="false"/>
   </outputs>
+  <expand macro="example_sub_foo_tests"/>
   <help><![CDATA[TODO: Write help]]></help>
+  <expand macro="citations"/>
 </tool>
 
-<tool id="example-sub.py_bar" name="example-sub.py bar" version="2.0">
+<tool name="example_sub_bar" id="example_sub_bar" version="2.0">
   <description/>
-  <stdio>
-    <exit_code level="fatal" range="1:"/>
-  </stdio>
-  <version_command>python example-sub.py bar --version</version_command>
+  <macros>
+    <import>example_sub_qux.xml</import>
+    <import>examples/macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command><![CDATA[python example-sub.py bar --version]]></version_command>
   <command><![CDATA[python example-sub.py bar $false
 #for $i in $repeat_1:
 --append $i.append
@@ -55,24 +95,31 @@ $true
 #if $mode and $mode is not None:
 --mode $mode
 #end if
+@EXAMPLE_SUB_QUX_INMACRO@
+@EXAMPLE_SUB_QUX_OUTMACRO@
 > $default]]></command>
   <inputs>
-    <param argument="--false" checked="false" label="Store a false" name="false" type="boolean" truevalue="--false" falsevalue=""/>
-    <repeat name="repeat_1" title="Repeated Variable">
-      <param argument="--append" label="Append a value" name="append" type="text"/>
+    <param label="Store a false" checked="false" type="boolean" name="false" argument="--false" truevalue="--false" falsevalue=""/>
+    <repeat title="Repeated Variable" name="repeat_1">
+      <param label="Append a value" type="text" name="append" argument="--append"/>
     </repeat>
-    <repeat max="2" min="2" name="repeat_2" title="repeat_title">
-      <param argument="--nargs2" label="nargs2" name="nargs2" optional="true" type="text"/>
+    <repeat title="repeat_title" min="2" max="2" name="repeat_2">
+      <param optional="true" label="nargs2" type="text" name="nargs2" argument="--nargs2"/>
     </repeat>
-    <param argument="--mode" label="Author did not provide help for this parameter... " name="mode" optional="true" type="select">
+    <param optional="true" label="Author did not provide help for this parameter... " type="select" name="mode" argument="--mode">
       <option value="paper">paper</option>
       <option value="rock">rock</option>
       <option selected="true" value="scissors">scissors</option>
     </param>
+    <expand macro="example_sub_qux_inmacro"/>
   </inputs>
   <outputs>
-    <data format="txt" hidden="false" name="default"/>
+    <expand macro="example_sub_qux_outmacro"/>
+    <data name="default" format="txt" hidden="false"/>
   </outputs>
+  <expand macro="example_sub_bar_tests"/>
   <help><![CDATA[TODO: Write help]]></help>
+  <expand macro="citations"/>
 </tool>
 
+</root>
diff --git a/examples/example-sub-bar.xml b/examples/example-sub/example_sub_bar.xml
similarity index 53%
rename from examples/example-sub-bar.xml
rename to examples/example-sub/example_sub_bar.xml
index e2462ee..386e986 100644
--- a/examples/example-sub-bar.xml
+++ b/examples/example-sub/example_sub_bar.xml
@@ -1,8 +1,12 @@
-<tool name="example-sub.py bar" id="example-sub.py_bar" version="2.0">
+<tool name="example_sub_bar" id="example_sub_bar" version="2.0">
   <description/>
-  <stdio>
-    <exit_code range="1:" level="fatal"/>
-  </stdio>
+  <macros>
+    <import>example_sub_qux.xml</import>
+    <import>examples/macros.xml</import>
+    <import>examples/macros_tests.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
   <version_command><![CDATA[python example-sub.py bar --version]]></version_command>
   <command><![CDATA[python example-sub.py bar $false
 #for $i in $repeat_1:
@@ -15,24 +19,29 @@
 #if $mode and $mode is not None:
 --mode $mode
 #end if
+@EXAMPLE_SUB_QUX_INMACRO@
+@EXAMPLE_SUB_QUX_OUTMACRO@
 > $default]]></command>
   <inputs>
     <param label="Store a false" checked="false" type="boolean" name="false" argument="--false" truevalue="--false" falsevalue=""/>
     <repeat title="Repeated Variable" name="repeat_1">
       <param label="Append a value" type="text" name="append" argument="--append"/>
     </repeat>
-    <repeat max="2" min="2" title="repeat_title" name="repeat_2">
-      <param label="nargs2" optional="true" type="text" name="nargs2" argument="--nargs2"/>
+    <repeat title="repeat_title" min="2" max="2" name="repeat_2">
+      <param optional="true" label="nargs2" type="text" name="nargs2" argument="--nargs2"/>
     </repeat>
-    <param label="Author did not provide help for this parameter... " optional="true" type="select" name="mode" argument="--mode">
+    <param optional="true" label="Author did not provide help for this parameter... " type="select" name="mode" argument="--mode">
       <option value="paper">paper</option>
       <option value="rock">rock</option>
       <option selected="true" value="scissors">scissors</option>
     </param>
+    <expand macro="example_sub_qux_inmacro"/>
   </inputs>
   <outputs>
-    <data hidden="false" format="txt" name="default"/>
+    <expand macro="example_sub_qux_outmacro"/>
+    <data name="default" format="txt" hidden="false"/>
   </outputs>
+  <expand macro="example_sub_bar_tests"/>
   <help><![CDATA[TODO: Write help]]></help>
+  <expand macro="citations"/>
 </tool>
-
diff --git a/examples/example-sub/example_sub_baz.xml b/examples/example-sub/example_sub_baz.xml
new file mode 100644
index 0000000..debf8e3
--- /dev/null
+++ b/examples/example-sub/example_sub_baz.xml
@@ -0,0 +1,12 @@
+<macros>
+  <token name="EXAMPLE_SUB_BAZ_INMACRO"><![CDATA[--baz '$baz'
+@EXAMPLE_SUB_QUX_INMACRO@]]></token>
+  <token name="EXAMPLE_SUB_BAZ_OUTMACRO"><![CDATA[@EXAMPLE_SUB_QUX_OUTMACRO@]]></token>
+  <xml name="example_sub_baz_inmacro">
+    <param optional="true" label="baz help" type="text" name="baz" argument="--baz"/>
+    <expand macro="example_sub_qux_inmacro"/>
+  </xml>
+  <xml name="example_sub_baz_outmacro">
+    <expand macro="example_sub_qux_outmacro"/>
+  </xml>
+</macros>
diff --git a/examples/example-sub-foo.xml b/examples/example-sub/example_sub_foo.xml
similarity index 53%
rename from examples/example-sub-foo.xml
rename to examples/example-sub/example_sub_foo.xml
index 8eacac6..46c7b71 100644
--- a/examples/example-sub-foo.xml
+++ b/examples/example-sub/example_sub_foo.xml
@@ -1,8 +1,13 @@
-<tool name="example-sub.py foo" id="example-sub.py_foo" version="1.0">
+<tool name="example_sub_foo" id="example_sub_foo" version="1.0">
   <description/>
-  <stdio>
-    <exit_code range="1:" level="fatal"/>
-  </stdio>
+  <macros>
+    <import>example_sub_baz.xml</import>
+    <import>example_sub_qux.xml</import>
+    <import>examples/macros.xml</import>
+    <import>examples/macros_tests.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
   <version_command><![CDATA[python example-sub.py foo --version]]></version_command>
   <command><![CDATA[python example-sub.py foo $keyword
 
@@ -12,29 +17,38 @@
 $sum
 
 #if $foo and $foo is not None:
---foo $foo
+--foo '$foo'
 #end if
 
 #set repeat_var_4 = '" "'.join([ str($var.bar) for $var in $repeat_4 ])
 --bar "$repeat_var_4"
 
 $true
+@EXAMPLE_SUB_BAZ_INMACRO@
+@EXAMPLE_SUB_QUX_INMACRO@
+@EXAMPLE_SUB_BAZ_OUTMACRO@
+@EXAMPLE_SUB_QUX_OUTMACRO@
 > $default]]></command>
   <inputs>
     <param label="action keyword" type="text" name="keyword"/>
-    <repeat min="1" title="repeat_title" name="repeat_2">
+    <repeat title="repeat_title" min="1" name="repeat_2">
       <param label="an integer for the accumulator" value="0" type="integer" name="integers"/>
     </repeat>
     <param label="sum the integers (default: find the max)" checked="false" type="boolean" name="sum" argument="--sum" truevalue="--sum" falsevalue=""/>
-    <param label="foo help" optional="true" type="text" name="foo" argument="--foo"/>
+    <param optional="true" label="foo help" type="text" name="foo" argument="--foo"/>
     <repeat title="repeat_title" name="repeat_4">
-      <param label="BAR!" optional="true" value="1" type="text" name="bar" argument="--bar"/>
+      <param optional="true" label="BAR!" value="1" type="text" name="bar" argument="--bar"/>
     </repeat>
     <param label="Store a true" checked="false" type="boolean" name="true" argument="--true" truevalue="--true" falsevalue=""/>
+    <expand macro="example_sub_baz_inmacro"/>
+    <expand macro="example_sub_qux_inmacro"/>
   </inputs>
   <outputs>
-    <data hidden="false" format="txt" name="default"/>
+    <expand macro="example_sub_baz_outmacro"/>
+    <expand macro="example_sub_qux_outmacro"/>
+    <data name="default" format="txt" hidden="false"/>
   </outputs>
+  <expand macro="example_sub_foo_tests"/>
   <help><![CDATA[TODO: Write help]]></help>
+  <expand macro="citations"/>
 </tool>
-
diff --git a/examples/example-sub/example_sub_qux.xml b/examples/example-sub/example_sub_qux.xml
new file mode 100644
index 0000000..264e043
--- /dev/null
+++ b/examples/example-sub/example_sub_qux.xml
@@ -0,0 +1,8 @@
+<macros>
+  <token name="EXAMPLE_SUB_QUX_INMACRO"><![CDATA[--qux '$qux']]></token>
+  <token name="EXAMPLE_SUB_QUX_OUTMACRO"><![CDATA[]]></token>
+  <xml name="example_sub_qux_inmacro">
+    <param optional="true" label="qux help" type="text" name="qux" argument="--qux"/>
+  </xml>
+  <xml name="example_sub_qux_outmacro"/>
+</macros>
diff --git a/examples/example.xml b/examples/example.xml
index ccaba3f..5839e5b 100644
--- a/examples/example.xml
+++ b/examples/example.xml
@@ -1,8 +1,10 @@
-<tool id="example.py" name="example.py" version="2.0">
+<tool name="example" id="example" version="2.0">
   <description>Process some integers.</description>
-  <stdio>
-    <exit_code level="fatal" range="1:"/>
-  </stdio>
+  <macros>
+    <import>examples/macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
   <version_command><![CDATA[python example.py --version]]></version_command>
   <command><![CDATA[python example.py $keyword
 
@@ -12,7 +14,7 @@
 $sum
 
 #if $foo and $foo is not None:
---foo $foo
+--foo '$foo'
 #end if
 
 #set repeat_var_4 = '" "'.join([ str($var.bar) for $var in $repeat_4 ])
@@ -32,32 +34,34 @@ $false
 #end if
 > $default]]></command>
   <inputs>
-    <param label="action keyword" name="keyword" type="text"/>
-    <repeat min="1" name="repeat_2" title="repeat_title">
-      <param label="an integer for the accumulator" name="integers" type="integer" value="0"/>
+    <param label="action keyword" type="text" name="keyword"/>
+    <repeat title="repeat_title" min="1" name="repeat_2">
+      <param label="an integer for the accumulator" value="0" type="integer" name="integers"/>
     </repeat>
-    <param argument="--sum" checked="false" label="sum the integers (default: find the max)" name="sum" type="boolean" truevalue="--sum" falsevalue=""/>
-    <param argument="--foo" label="foo help" name="foo" optional="true" type="text"/>
-    <repeat name="repeat_4" title="repeat_title">
-      <param argument="--bar" label="BAR!" name="bar" optional="true" type="text" value="1"/>
+    <param label="sum the integers (default: find the max)" checked="false" type="boolean" name="sum" argument="--sum" truevalue="--sum" falsevalue=""/>
+    <param optional="true" label="foo help" type="text" name="foo" argument="--foo"/>
+    <repeat title="repeat_title" name="repeat_4">
+      <param optional="true" label="BAR!" value="1" type="text" name="bar" argument="--bar"/>
     </repeat>
-    <param argument="--true" checked="false" label="Store a true" name="true" type="boolean" truevalue="--true" falsevalue=""/>
-    <param argument="--false" checked="false" label="Store a false" name="false" type="boolean" truevalue="--false" falsevalue=""/>
-    <repeat name="repeat_5" title="Repeated Variable">
-      <param argument="--append" label="Append a value" name="append" type="text"/>
+    <param label="Store a true" checked="false" type="boolean" name="true" argument="--true" truevalue="--true" falsevalue=""/>
+    <param label="Store a false" checked="false" type="boolean" name="false" argument="--false" truevalue="--false" falsevalue=""/>
+    <repeat title="Repeated Variable" name="repeat_5">
+      <param label="Append a value" type="text" name="append" argument="--append"/>
     </repeat>
-    <repeat max="2" min="2" name="repeat_6" title="repeat_title">
-      <param argument="--nargs2" label="nargs2" name="nargs2" optional="true" type="text"/>
+    <repeat title="repeat_title" min="2" max="2" name="repeat_6">
+      <param optional="true" label="nargs2" type="text" name="nargs2" argument="--nargs2"/>
     </repeat>
-    <param argument="--mode" label="Author did not provide help for this parameter... " name="mode" optional="true" type="select">
+    <param optional="true" label="Author did not provide help for this parameter... " type="select" name="mode" argument="--mode">
       <option value="paper">paper</option>
       <option value="rock">rock</option>
       <option selected="true" value="scissors">scissors</option>
     </param>
   </inputs>
   <outputs>
-    <data format="txt" hidden="false" name="default"/>
+    <data name="default" format="txt" hidden="false"/>
   </outputs>
+  <expand macro="example_tests"/>
   <help><![CDATA[here's some epilog text]]></help>
+  <expand macro="citations"/>
 </tool>
 
diff --git a/examples/macros.xml b/examples/macros.xml
new file mode 100644
index 0000000..9bd6ed4
--- /dev/null
+++ b/examples/macros.xml
@@ -0,0 +1,27 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+  <token name="@TOOL_VERSION@">4.4</token>
+  <token name="@GALAXY_VERSION@">0</token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">bash</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <xml name="stdio">
+    <stdio>
+      <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
+      <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
+      <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
+    </stdio>
+  </xml>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">doi:10.1093/nar/gkw343</citation>
+    </citations>
+  </xml>
+  <xml name="example_tests">
+    <tests>
+  </tests>
+  </xml>
+</macros>
diff --git a/examples/macros_tests.xml b/examples/macros_tests.xml
new file mode 100644
index 0000000..ba6ea77
--- /dev/null
+++ b/examples/macros_tests.xml
@@ -0,0 +1,16 @@
+<macros>
+  <xml name="example_sub_foo_tests">
+    <tests>
+      <test expect_exit_code="0">
+          <output name="default" ftype="txt"/>
+      </test>
+    </tests>
+  </xml>
+  <xml name="example_sub_bar_tests">
+    <tests>
+      <test expect_exit_code="0">
+          <output name="default" ftype="txt"/>
+      </test>
+    </tests>
+  </xml>
+</macros>