diff --git a/examples/tool.xml b/examples/tool.xml
index 2347717..9e11993 100644
--- a/examples/tool.xml
+++ b/examples/tool.xml
@@ -5,10 +5,6 @@
     <requirement version="1.0.0" type="package">samtools</requirement>
     <container type="docker">one_super_image</container>
   </requirements>
-  <stdio>
-    <exit_code range="1:" level="fatal"/>
-  </stdio>
-  <expand macro="stdio"/>
   <version_command><![CDATA[aragorn.exe --version]]></version_command>
   <command><![CDATA[aragorn.exe $flag
 -float $float_section.float
diff --git a/galaxyxml/__init__.py b/galaxyxml/__init__.py
index 38fc4a7..8aeb72d 100644
--- a/galaxyxml/__init__.py
+++ b/galaxyxml/__init__.py
@@ -1,7 +1,4 @@
-from builtins import (
-    object,
-    str
-)
+from builtins import object, str
 
 from lxml import etree
 
diff --git a/galaxyxml/tool/__init__.py b/galaxyxml/tool/__init__.py
index c636cf2..12c9083 100644
--- a/galaxyxml/tool/__init__.py
+++ b/galaxyxml/tool/__init__.py
@@ -2,15 +2,7 @@
 import logging
 
 from galaxyxml import GalaxyXML, Util
-from galaxyxml.tool.parameters import (
-    Expand,
-    Import,
-    Inputs,
-    Macro,
-    Macros,
-    Outputs,
-    XMLParam
-)
+from galaxyxml.tool.parameters import Expand, Import, Inputs, Macro, Macros, Outputs, XMLParam, Command
 
 from lxml import etree
 
@@ -37,18 +29,21 @@ def __init__(
         version_command="interpreter filename.exe --version",
         command_override=None,
         macros=[],
+        profile=None,
     ):
 
         self.id = id
         self.executable = executable
         self.interpreter = interpreter
         self.command_override = command_override
+        self.profile = profile
         kwargs = {
             "name": name,
             "id": id,
             "version": version,
             "hidden": hidden,
             "workflow_compatible": workflow_compatible,
+            "profile": profile
         }
         self.version_command = version_command
 
@@ -81,6 +76,7 @@ def __init__(
                 self.macros.append(Import(m))
         self.inputs = Inputs()
         self.outputs = Outputs()
+        self.command = Command()
 
     def add_comment(self, comment_txt):
         comment = etree.Comment(comment_txt)
@@ -134,13 +130,11 @@ def export(self, keep_old_command=False):
             stdio_element = export_xml.stdios
         except Exception:
             stdio_element = None
-        if not stdio_element:
-            stdio_element = etree.SubElement(export_xml.root, "stdio")
-            etree.SubElement(stdio_element, "exit_code", range="1:", level="fatal")
-        try:
-            export_xml.append(stdio_element)
-        except Exception:
-            export_xml.append(Expand(macro="stdio"))
+        if stdio_element:
+            try:
+                export_xml.append(stdio_element)
+            except Exception:
+                export_xml.append(Expand(macro="stdio"))
 
         # Append version command
         export_xml.append_version_command()
@@ -158,25 +152,30 @@ def export(self, keep_old_command=False):
                 command_line.append(export_xml.outputs.cli())
             except Exception:
                 pass
-        # Steal interpreter from kwargs
-        command_kwargs = {}
-        if export_xml.interpreter is not None:
-            command_kwargs["interpreter"] = export_xml.interpreter
         # Add command section
-        command_node = etree.SubElement(export_xml.root, "command", **command_kwargs)
+        command_node_text = None
         if keep_old_command:
             if getattr(self, "command", None):
-                command_node.text = etree.CDATA(export_xml.command)
+                command_node_text = etree.CDATA(export_xml.command)
             else:
                 logger.warning("The tool does not have any old command stored. Only the command line is written.")
-                command_node.text = export_xml.executable
+                command_node_text = export_xml.executable
         else:
             if self.command_override:
                 actual_cli = export_xml.clean_command_string(command_line)
             else:
-                actual_cli = "%s %s" % (export_xml.executable, export_xml.clean_command_string(command_line),)
-            command_node.text = etree.CDATA(actual_cli.strip())
-        export_xml.append(command_node)
+                actual_cli = "%s %s" % (
+                    export_xml.executable,
+                    export_xml.clean_command_string(command_line),
+                )
+            command_node_text = actual_cli.strip()
+        export_xml.command_line = command_node_text
+        try:
+            command_element = export_xml.command
+        except Exception:
+            command_element = etree.SubElement(export_xml.root, "command", detect_errors=None)
+        command_element.node.text = etree.CDATA(command_node_text)
+        export_xml.append(command_element)
 
         try:
             export_xml.append(export_xml.configfiles)
@@ -226,13 +225,13 @@ class MacrosTool(Tool):
 
     TODO all other elements, like requirements are currently ignored
     """
+
     def __init__(self, *args, **kwargs):
         super(MacrosTool, self).__init__(*args, **kwargs)
         self.root = etree.Element('macros')
         self.inputs = Macro("%s_inmacro" % self.id)
         self.outputs = Macro("%s_outmacro" % self.id)
 
-
     def export(self, keep_old_command=False):  # noqa
 
         export_xml = copy.deepcopy(self)
diff --git a/galaxyxml/tool/import_xml.py b/galaxyxml/tool/import_xml.py
index 28e9178..805c0f2 100644
--- a/galaxyxml/tool/import_xml.py
+++ b/galaxyxml/tool/import_xml.py
@@ -27,7 +27,6 @@ def _init_tool(self, xml_root):
                 description = child.text
             elif child.tag == "command":
                 executable = child.text.split()[0]
-                command = child.text
             elif child.tag == "version_command":
                 version_cmd = child.text
 
@@ -43,7 +42,6 @@ def _init_tool(self, xml_root):
             workflow_compatible=xml_root.attrib.get("workflow_compatible", True),
             version_command=version_cmd,
         )
-        tool.command = command
         return tool
 
     def _load_description(self, tool, desc_root):
@@ -77,21 +75,28 @@ def _load_stdio(self, tool, stdio_root):
         """
         tool.stdios = gxtp.Stdios()
         for std in stdio_root:
-            slevel = std.attrib['level']
-            srange = std.attrib['range']
+            slevel = std.attrib["level"]
+            srange = std.attrib["range"]
             tool.stdios.append(gxtp.Stdio(level=slevel, range=srange))
         logger.info("<stdio> loaded.")
 
-    def _load_command(self, tool, desc_root):
+    def _load_command(self, tool, command_root):
         """
-        <command> is already loaded during initiation.
-
         :param tool: Tool object from galaxyxml.
         :type tool: :class:`galaxyxml.tool.Tool`
         :param desc_root: root of <command> tag.
         :type desc_root: :class:`xml.etree._Element`
         """
-        logger.info("<command> is loaded during initiation of the object.")
+        try:
+            detect_errors = command_root.attrib['detect_errors']
+        except KeyError:
+            detect_errors = None
+        ctext = command_root.text
+        command = gxtp.Command(detect_errors=detect_errors)
+        command.node.text = ctext
+        tool.command_line = ctext
+        tool.command = command
+        tool.executable = ctext.split()[0]
 
     def _load_help(self, tool, help_root):
         """
@@ -727,11 +732,12 @@ def _load_element(self, test_root, element_root):
         :param repeat_root: root of <output_collection> tag.
         :param repeat_root: :class:`xml.etree._Element`
         """
-        test_root.append(gxtp.TestOCElement(
-            name=element_root.attrib.get("name", None),
-            ftype=element_root.attrib.get("ftype", None),
-            file=element_root.attrib.get("file", None)
-        )
+        test_root.append(
+            gxtp.TestOCElement(
+                name=element_root.attrib.get("name", None),
+                ftype=element_root.attrib.get("ftype", None),
+                file=element_root.attrib.get("file", None),
+            )
         )
 
     def _load_repeat(self, test_root, repeat_root):
@@ -747,7 +753,7 @@ def _load_repeat(self, test_root, repeat_root):
             repeat_root.attrib.get("title", None),
             min=repeat_root.attrib.get("min", None),
             max=repeat_root.attrib.get("max", None),
-            default=repeat_root.attrib.get("default", None)
+            default=repeat_root.attrib.get("default", None),
         )
         # Deal with child nodes
         self.load_inputs(repeat, repeat_root)
diff --git a/galaxyxml/tool/parameters/__init__.py b/galaxyxml/tool/parameters/__init__.py
index ee9e647..04c0b53 100644
--- a/galaxyxml/tool/parameters/__init__.py
+++ b/galaxyxml/tool/parameters/__init__.py
@@ -1,9 +1,5 @@
 import logging
-from builtins import (
-    object,
-    str
-)
-
+from builtins import (object, str)
 from galaxy.tool_util.parser.util import _parse_name
 
 from galaxyxml import Util
@@ -79,6 +75,14 @@ def command_line(self, mako_path=None):
         return None
 
 
+class Command(XMLParam):
+    name = "command"
+
+    def __init__(self, detect_errors=None, **kwargs):
+        params = Util.clean_kwargs(locals().copy())
+        super(Command, self).__init__(**params)
+
+
 class Stdios(XMLParam):
     name = "stdio"
 
@@ -129,6 +133,7 @@ class Expand(XMLParam):
     """
     <expand macro="...">
     """
+
     name = "expand"
 
     def __init__(self, macro):
@@ -151,6 +156,7 @@ class ExpandIO(Expand):
     but an additional token with the same name but in upper case is added to
     the command section. can only be used in Inputs and Outputs
     """
+
     name = "expand"
 
     def __init__(self, macro):
@@ -170,8 +176,7 @@ def __init__(self, **kwargs):
         self.node = etree.Element(self.name)
 
     def acceptable_child(self, child):
-        return isinstance(child, RequestParamTranslation) \
-            or isinstance(child, Expand)
+        return isinstance(child, RequestParamTranslation) or isinstance(child, Expand)
 
 
 class RequestParam(XMLParam):
@@ -185,8 +190,7 @@ def __init__(self, galaxy_name, remote_name, missing, **kwargs):
         super(RequestParam, self).__init__(**params)
 
     def acceptable_child(self, child):
-        return isinstance(child, AppendParam) and self.galaxy_name == "URL" \
-            or isinstance(child, Expand)
+        return isinstance(child, AppendParam) and self.galaxy_name == "URL" or isinstance(child, Expand)
 
 
 class AppendParam(XMLParam):
@@ -215,8 +219,7 @@ class EdamOperations(XMLParam):
     name = "edam_operations"
 
     def acceptable_child(self, child):
-        return issubclass(type(child), EdamOperation) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), EdamOperation) or isinstance(child, Expand)
 
     def has_operation(self, edam_operation):
         """
@@ -242,8 +245,7 @@ class EdamTopics(XMLParam):
     name = "edam_topics"
 
     def acceptable_child(self, child):
-        return issubclass(type(child), EdamTopic) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), EdamTopic) or isinstance(child, Expand)
 
     def has_topic(self, edam_topic):
         """
@@ -270,9 +272,7 @@ class Requirements(XMLParam):
     # This bodes to be an issue -__-
 
     def acceptable_child(self, child):
-        return issubclass(type(child), Requirement) \
-            or issubclass(type(child), Container) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), Requirement) or issubclass(type(child), Container) or isinstance(child, Expand)
 
 
 class Requirement(XMLParam):
@@ -302,9 +302,11 @@ class Configfiles(XMLParam):
     name = "configfiles"
 
     def acceptable_child(self, child):
-        return issubclass(type(child), Configfile) \
-            or issubclass(type(child), ConfigfileDefaultInputs) \
+        return (
+            issubclass(type(child), Configfile)
+            or issubclass(type(child), ConfigfileDefaultInputs)
             or isinstance(child, Expand)
+        )
 
 
 class Configfile(XMLParam):
@@ -337,18 +339,20 @@ def __init__(self, action=None, check_value=None, method=None, target=None, ngin
         super(Inputs, self).__init__(**params)
 
     def acceptable_child(self, child):
-        return issubclass(type(child), InputParameter) \
-            or issubclass(type(child), Expand) \
+        return (
+            issubclass(type(child), InputParameter)
+            or issubclass(type(child), Expand)
             or issubclass(type(child), ExpandIO)
+        )
 
 
 class InputParameter(XMLParam):
     def __init__(self, name, **kwargs):
         # TODO: look at
-        if "argument" in kwargs and kwargs['argument']:
-            self.flag_identifier = kwargs['argument'].lstrip()
-            self.num_dashes = len(kwargs['argument']) - len(self.flag_identifier)
-            self.mako_identifier = _parse_name(name, kwargs['argument'])
+        if "argument" in kwargs and kwargs["argument"]:
+            self.flag_identifier = kwargs["argument"].lstrip()
+            self.num_dashes = len(kwargs["argument"]) - len(self.flag_identifier)
+            self.mako_identifier = _parse_name(name, kwargs["argument"])
         else:
             self.flag_identifier = name
             self.mako_identifier = name
@@ -379,8 +383,8 @@ def __init__(self, name, **kwargs):
             if len(self.flag()) > 0:
                 if kwargs["label"] is None:
                     kwargs["label"] = "Author did not provide help for this parameter... "
-#                 if not self.positional and "argument" not in kwargs:
-#                     kwargs["argument"] = self.flag()
+        #                 if not self.positional and "argument" not in kwargs:
+        #                     kwargs["argument"] = self.flag()
 
         super(InputParameter, self).__init__(**kwargs)
 
@@ -442,8 +446,7 @@ def command_line(self, mako_path=None):
         return "\n".join(cli)
 
     def acceptable_child(self, child):
-        return issubclass(type(child), InputParameter) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), InputParameter) or isinstance(child, Expand)
 
 
 class Repeat(InputParameter):
@@ -460,8 +463,7 @@ def command_line_after(self):
         return "#end for"
 
     def acceptable_child(self, child):
-        return issubclass(type(child), InputParameter) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), InputParameter) or isinstance(child, Expand)
 
     def command_line_actual(self, mako_path):
         lines = []
@@ -486,7 +488,8 @@ def acceptable_child(self, child):
             return True
         else:
             return False
-#         return issubclass(type(child), InputParameter) and not isinstance(child, Conditional)
+
+    #         return issubclass(type(child), InputParameter) and not isinstance(child, Conditional)
 
     def command_line(self, mako_path=None):
         lines = []
@@ -495,7 +498,7 @@ def command_line(self, mako_path=None):
                 continue
             lines.append('#if str(%s) == "%s"' % (self.children[0].mako_name(mako_path), c.value))
             lines.append(c.cli())
-            lines.append('#end if')
+            lines.append("#end if")
         return "\n".join(lines)
 
     def validate(self):
@@ -511,8 +514,7 @@ def __init__(self, value):
         super(When, self).__init__(None, **params)
 
     def acceptable_child(self, child):
-        return issubclass(type(child), InputParameter) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), InputParameter) or isinstance(child, Expand)
 
 
 class Param(InputParameter):
@@ -521,18 +523,16 @@ class Param(InputParameter):
     # This...isn't really valid as-is, and shouldn't be used.
     def __init__(self, name, argument=None, value=None, optional=None, label=None, help=None, **kwargs):
         params = Util.clean_kwargs(locals().copy())
-        params = dict([("name", params["name"]),
-                      ("argument", params["argument"]),
-                      ("type", self.type)] + list(params.items()))
+        params = dict(
+            [("name", params["name"]), ("argument", params["argument"]), ("type", self.type)] + list(params.items())
+        )
         super(Param, self).__init__(**params)
 
         if type(self) == Param:
             raise Exception("Param class is not an actual parameter type, use a subclass of Param")
 
     def acceptable_child(self, child):
-        return issubclass(type(child), InputParameter) \
-            or isinstance(child, ValidatorParam) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), InputParameter) or isinstance(child, ValidatorParam) or isinstance(child, Expand)
 
 
 class TextParam(Param):
@@ -571,7 +571,16 @@ class BooleanParam(Param):
     type = "boolean"
 
     def __init__(
-        self, name, argument=None, optional=None, checked=False, truevalue=None, falsevalue=None, label=None, help=None, **kwargs
+        self,
+        name,
+        argument=None,
+        optional=None,
+        checked=False,
+        truevalue=None,
+        falsevalue=None,
+        label=None,
+        help=None,
+        **kwargs,
     ):
         params = Util.clean_kwargs(locals().copy())
 
@@ -638,9 +647,7 @@ def __init__(
                 self.append(SelectOption(k, v, selected=selected))
 
     def acceptable_child(self, child):
-        return issubclass(type(child), SelectOption) \
-            or issubclass(type(child), Options) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), SelectOption) or issubclass(type(child), Options) or isinstance(child, Expand)
 
 
 class SelectOption(InputParameter):
@@ -666,9 +673,7 @@ def __init__(self, from_dataset=None, from_file=None, from_data_table=None, from
         super(Options, self).__init__(None, **params)
 
     def acceptable_child(self, child):
-        return issubclass(type(child), Column) \
-            or issubclass(type(child), Filter) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), Column) or issubclass(type(child), Filter) or isinstance(child, Expand)
 
 
 class Column(InputParameter):
@@ -724,15 +729,16 @@ class Outputs(XMLParam):
     name = "outputs"
 
     def acceptable_child(self, child):
-        return isinstance(child, OutputData) \
-            or isinstance(child, OutputCollection) \
-            or isinstance(child, Expand) \
+        return (
+            isinstance(child, OutputData)
+            or isinstance(child, OutputCollection)
+            or isinstance(child, Expand)
             or isinstance(child, ExpandIO)
+        )
 
 
 class OutputData(XMLParam):
-    """Copypasta of InputParameter, needs work
-    """
+    """Copypasta of InputParameter, needs work"""
 
     name = "data"
 
@@ -774,10 +780,12 @@ def flag(self):
         return flag + self.mako_identifier
 
     def acceptable_child(self, child):
-        return isinstance(child, OutputFilter) \
-            or isinstance(child, ChangeFormat) \
-            or isinstance(child, DiscoverDatasets) \
+        return (
+            isinstance(child, OutputFilter)
+            or isinstance(child, ChangeFormat)
+            or isinstance(child, DiscoverDatasets)
             or isinstance(child, Expand)
+        )
 
 
 class OutputFilter(XMLParam):
@@ -801,8 +809,7 @@ def __init__(self, **kwargs):
         super(ChangeFormat, self).__init__(**params)
 
     def acceptable_child(self, child):
-        return isinstance(child, ChangeFormatWhen) \
-            or isinstance(child, Expand)
+        return isinstance(child, ChangeFormatWhen) or isinstance(child, Expand)
 
 
 class ChangeFormatWhen(XMLParam):
@@ -861,19 +868,20 @@ class Tests(XMLParam):
     name = "tests"
 
     def acceptable_child(self, child):
-        return issubclass(type(child), Test) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), Test) or isinstance(child, Expand)
 
 
 class Test(XMLParam):
     name = "test"
 
     def acceptable_child(self, child):
-        return isinstance(child, TestParam) \
-            or isinstance(child, TestOutput) \
-            or isinstance(child, TestOutputCollection) \
-            or isinstance(child, TestRepeat) \
+        return (
+            isinstance(child, TestParam)
+            or isinstance(child, TestOutput)
+            or isinstance(child, TestOutputCollection)
+            or isinstance(child, TestRepeat)
             or isinstance(child, Expand)
+        )
 
 
 class TestParam(XMLParam):
@@ -964,9 +972,11 @@ def __init__(
         super(TestRepeat, self).__init__(**params)
 
     def acceptable_child(self, child):
-        return issubclass(type(child), TestParam) \
-            or issubclass(type(child), TestOutput) \
+        return (
+            issubclass(type(child), TestParam)
+            or issubclass(type(child), TestOutput)
             or issubclass(type(child), TestOutputCollection)
+        )
 
     def command_line_before(self, mako_path):
         return "<repeat name = '%s'>" % self.name
@@ -985,8 +995,7 @@ class Citations(XMLParam):
     name = "citations"
 
     def acceptable_child(self, child):
-        return issubclass(type(child), Citation) \
-            or isinstance(child, Expand)
+        return issubclass(type(child), Citation) or isinstance(child, Expand)
 
     def has_citation(self, type, value):
         """
@@ -996,8 +1005,7 @@ def has_citation(self, type, value):
         :type value: STRING
         """
         for citation in self.children:
-            if citation.node.attrib['type'] == type \
-               and citation.node.text == value:
+            if citation.node.attrib["type"] == type and citation.node.text == value:
                 return True
         return False
 
diff --git a/setup.py b/setup.py
index 762a7d0..af18d01 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 
 setup(
     name="galaxyxml",
-    version="0.4.14",
+    version="0.4.15",
     description="Galaxy XML generation library",
     author="Helena Rasche",
     author_email="hxr@hx42.org",
diff --git a/test/import_xml.xml b/test/import_xml.xml
index c1656d6..132118e 100644
--- a/test/import_xml.xml
+++ b/test/import_xml.xml
@@ -18,7 +18,8 @@
     <exit_code level="fatal" range="1:"/>
   </stdio>
   <version_command>v_command</version_command>
-  <command><![CDATA[command]]></command>
+  <command><![CDATA[command]]>
+  </command>
   <inputs>
     <param name="interval_file" type="data" format="interval" label="near intervals in"/>
     <param checked="false" help="a help" label="a label" name="bool" type="boolean" truevalue="--bool" falsevalue=""/>
diff --git a/test/unit_test_import_xml.py b/test/unit_test_import_xml.py
index 7560006..4f4d0d7 100644
--- a/test/unit_test_import_xml.py
+++ b/test/unit_test_import_xml.py
@@ -31,6 +31,17 @@ def test_override(self):
         self.assertTrue(co in exml)
 
 
+class TestCommand(TestImport):
+    def test_command(self):
+        try:
+            de = self.tool.command.node.attrib["detect_errors"]
+        except KeyError:
+            de = None
+        self.assertEqual(de, None)
+        ctext = self.tool.command.node.text
+        self.assertEqual(ctext.strip(), "command")
+
+
 class TestImportXml(TestImport):
     def test_init_tool(self):
         xml_root = self.tool.root
diff --git a/tox.ini b/tox.ini
index 61e9aca..27d8501 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,3 +1,22 @@
+[tox]
+env_list = py{38,310}-lint, py{38,310}-test
+source_dir = galaxyxml
+test_dir = test
+
 [flake8]
 max-line-length = 230
 max-complexity = 10
+ignore = E2,E3,E4,E5,W3,W505,C901,E501,E128,E203,E402,E501,E741,W503,W504,
+exclude = .ci, .git, .tox, .venv
+
+
+[testenv]
+deps =
+	lint: flake8
+	lint: black
+	test: pytest
+
+commands =
+	lint: flake8
+    lint: black --check --diff .
+	test: pytest