| Previous changeset 34:5052ac89c036 (2020-08-08) Next changeset 36:ce2b1f8ea68d (2020-08-10) |
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Commit message:
added patched galaxyxml code temporarily until PR accepted |
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added:
toolfactory/__init__.py toolfactory/galaxyxml/__init__.py toolfactory/galaxyxml/tool/__init__.py toolfactory/galaxyxml/tool/import_xml.py toolfactory/galaxyxml/tool/parameters/__init__.py toolfactory/sample_toolfactory_tools.ga |
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| diff -r 5052ac89c036 -r 5d38cb3d9be8 toolfactory/galaxyxml/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/__init__.py Sat Aug 08 19:55:55 2020 -0400 |
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| @@ -0,0 +1,66 @@ +from builtins import str +from builtins import object +from lxml import etree + + +class GalaxyXML(object): + + def __init__(self): + self.root = etree.Element('root') + + def export(self): + return etree.tostring(self.root, pretty_print=True, encoding='unicode') + + +class Util(object): + + @classmethod + def coerce(cls, data, kill_lists=False): + """Recursive data sanitisation + """ + if isinstance(data, dict): + return {k: cls.coerce(v, kill_lists=kill_lists) for k, v in + list(data.items()) if v is not None} + elif isinstance(data, list): + if kill_lists: + return cls.coerce(data[0]) + else: + return [cls.coerce(v, kill_lists=kill_lists) for v in data] + else: + return cls.coerce_value(data) + + @classmethod + def coerce_value(cls, obj): + """Make everything a string! + """ + if isinstance(obj, bool): + if obj: + return "true" + else: + return "false" + elif isinstance(obj, str): + return obj + else: + return str(obj) + + @classmethod + def clean_kwargs(cls, params, final=False): + if 'kwargs' in params: + kwargs = params['kwargs'] + for k in kwargs: + params[k] = kwargs[k] + del params['kwargs'] + if 'self' in params: + del params['self'] + + if '__class__' in params: + del params['__class__'] + + # There will be more params, it would be NICE to use a whitelist + # instead of a blacklist, but until we have more data let's just + # blacklist stuff we see commonly. + if final: + for blacklist in ('positional',): + if blacklist in params: + del params[blacklist] + return params |
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| diff -r 5052ac89c036 -r 5d38cb3d9be8 toolfactory/galaxyxml/tool/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/tool/__init__.py Sat Aug 08 19:55:55 2020 -0400 |
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| @@ -0,0 +1,172 @@ +import copy +import logging +from lxml import etree +from galaxyxml import Util, GalaxyXML +from galaxyxml.tool.parameters import XMLParam + +VALID_TOOL_TYPES = ('data_source', 'data_source_async') +VALID_URL_METHODS = ('get', 'post') + +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__name__) + + +class Tool(GalaxyXML): + + def __init__(self, name, id, version, description, executable, hidden=False, + tool_type=None, URL_method=None, workflow_compatible=True, + interpreter=None, version_command='interpreter filename.exe --version', + command_line_override=None): + + self.executable = executable + self.interpreter = interpreter + self.command_line_override = command_line_override + kwargs = { + 'name': name, + 'id': id, + 'version': version, + 'hidden': hidden, + 'workflow_compatible': workflow_compatible, + } + self.version_command = version_command + + # Remove some of the default values to make tools look a bit nicer + if not hidden: + del kwargs['hidden'] + if workflow_compatible: + del kwargs['workflow_compatible'] + + kwargs = Util.coerce(kwargs) + self.root = etree.Element('tool', **kwargs) + + if tool_type is not None: + if tool_type not in VALID_TOOL_TYPES: + raise Exception("Tool type must be one of %s" % + ','.join(VALID_TOOL_TYPES)) + else: + kwargs['tool_type'] = tool_type + + if URL_method is not None: + if URL_method in VALID_URL_METHODS: + kwargs['URL_method'] = URL_method + else: + raise Exception("URL_method must be one of %s" % + ','.join(VALID_URL_METHODS)) + + description_node = etree.SubElement(self.root, 'description') + description_node.text = description + + def add_comment(self, comment_txt): + comment = etree.Comment(comment_txt) + self.root.insert(0, comment) + + def append_version_command(self): + version_command = etree.SubElement(self.root, 'version_command') + try: + version_command.text = etree.CDATA(self.version_command) + except Exception: + pass + + def append(self, sub_node): + if issubclass(type(sub_node), XMLParam): + self.root.append(sub_node.node) + else: + self.root.append(sub_node) + + def clean_command_string(self, command_line): + clean = [] + for x in command_line: + if x is not [] and x is not ['']: + clean.append(x) + + return '\n'.join(clean) + + def export(self, keep_old_command=False): # noqa + + export_xml = copy.deepcopy(self) + + try: + export_xml.append(export_xml.edam_operations) + except Exception: + pass + + try: + export_xml.append(export_xml.edam_topics) + except Exception: + pass + + try: + export_xml.append(export_xml.requirements) + except Exception: + pass + + try: + export_xml.append(export_xml.configfiles) + except Exception: + pass + + if self.command_line_override != None: + command_line = self.command_line_override + else: + command_line = [] + try: + command_line.append(export_xml.inputs.cli()) + except Exception as e: + logger.warning(str(e)) + + try: + command_line.append(export_xml.outputs.cli()) + except Exception: + pass + + # Add stdio section + stdio = etree.SubElement(export_xml.root, 'stdio') + etree.SubElement(stdio, 'exit_code', range='1:', level='fatal') + + # Append version command + export_xml.append_version_command() + + # 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) + + if keep_old_command: + if getattr(self, 'command', None): + 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 + else: + actual_cli = "%s %s" % ( + export_xml.executable, export_xml.clean_command_string(command_line)) + command_node.text = etree.CDATA(actual_cli.strip()) + + try: + export_xml.append(export_xml.inputs) + except Exception: + pass + + try: + export_xml.append(export_xml.outputs) + except Exception: + pass + + try: + export_xml.append(export_xml.tests) + except Exception: + pass + + help_element = etree.SubElement(export_xml.root, 'help') + help_element.text = etree.CDATA(export_xml.help) + + try: + export_xml.append(export_xml.citations) + except Exception: + pass + + return super(Tool, export_xml).export() |
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| diff -r 5052ac89c036 -r 5d38cb3d9be8 toolfactory/galaxyxml/tool/import_xml.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/tool/import_xml.py Sat Aug 08 19:55:55 2020 -0400 |
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| b'@@ -0,0 +1,660 @@\n+import logging\n+import xml.etree.ElementTree as ET\n+import galaxyxml.tool as gxt\n+import galaxyxml.tool.parameters as gxtp\n+\n+logging.basicConfig(level=logging.INFO)\n+logger = logging.getLogger(__name__)\n+\n+\n+class GalaxyXmlParser(object):\n+ """\n+ Class to import content from an existing Galaxy XML wrapper.\n+ """\n+\n+ def _init_tool(self, xml_root):\n+ """\n+ Init tool from existing xml tool.\n+\n+ :param xml_root: root of the galaxy xml file.\n+ :type xml_root: :class:`xml.etree._Element`\n+ """\n+ version_cmd = None\n+ description = None\n+ for child in xml_root:\n+ if child.tag == \'description\':\n+ description = child.text\n+ elif child.tag == \'command\':\n+ executable = child.text.split()[0]\n+ command = child.text\n+ elif child.tag == \'version_command\':\n+ version_cmd = child.text\n+\n+ tool = gxt.Tool(xml_root.attrib[\'name\'],\n+ xml_root.attrib[\'id\'],\n+ xml_root.attrib.get(\'version\', None),\n+ description,\n+ executable,\n+ hidden=xml_root.attrib.get(\'hidden\', False),\n+ tool_type=xml_root.attrib.get(\'tool_type\', None),\n+ URL_method=xml_root.attrib.get(\'URL_method\', None),\n+ workflow_compatible=xml_root.attrib.get(\'workflow_compatible\', True),\n+ version_command=version_cmd)\n+ tool.command = command\n+ return tool\n+\n+ def _load_description(self, tool, desc_root):\n+ """\n+ <description> is already loaded during initiation.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param desc_root: root of <description> tag.\n+ :type desc_root: :class:`xml.etree._Element`\n+ """\n+ logger.info("<description> is loaded during initiation of the object.")\n+\n+ def _load_version_command(self, tool, vers_root):\n+ """\n+ <version_command> is already loaded during initiation.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param vers_root: root of <version_command> tag.\n+ :type vers_root: :class:`xml.etree._Element`\n+ """\n+ logger.info("<version_command> is loaded during initiation of the object.")\n+\n+ def _load_stdio(self, tool, stdio_root):\n+ """\n+ So far, <stdio> is automatically generated by galaxyxml.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param desc_root: root of <stdio> tag.\n+ :type desc_root: :class:`xml.etree._Element`\n+ """\n+ logger.info("<stdio> is not loaded but automatically generated by galaxyxml.")\n+\n+ def _load_command(self, tool, desc_root):\n+ """\n+ <command> is already loaded during initiation.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param desc_root: root of <command> tag.\n+ :type desc_root: :class:`xml.etree._Element`\n+ """\n+ logger.info("<command> is loaded during initiation of the object.")\n+\n+ def _load_help(self, tool, help_root):\n+ """\n+ Load the content of the <help> into the tool.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param requirements_root: root of <help> tag.\n+ :type requirements_root: :class:`xml.etree._Element`\n+ """\n+ tool.help = help_root.text\n+\n+ def _load_requirements(self, tool, requirements_root):\n+ """\n+ Add <requirements> to the tool.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param requirements_root: root of <requirements'..b' :param disc_root: root of <discover_datasets> tag.\n+ :param disc_root: :class:`xml.etree._Element`\n+ """\n+ root.append(gxtp.DiscoverDatasets(disc_root.attrib[\'pattern\'],\n+ directory=disc_root.attrib.get(\'directory\', None),\n+ format=disc_root.attrib.get(\'format\', None),\n+ ext=disc_root.attrib.get(\'ext\', None),\n+ visible=disc_root.attrib.get(\'visible\', None)))\n+\n+ def _load_filter(self, root, filter_root):\n+ """\n+ Add <filter> to root (<collection> or <data>).\n+\n+ :param root: root to append <collection> to.\n+ :param coll_root: root of <filter> tag.\n+ :param coll_root: :class:`xml.etree._Element`\n+ """\n+ root.append(gxtp.OutputFilter(filter_root.text))\n+\n+ def load_outputs(self, root, outputs_root):\n+ """\n+ Add <outputs> to the root.\n+\n+ :param root: root to attach <outputs> to (<tool>).\n+ :param tests_root: root of <outputs> tag.\n+ :type tests_root: :class:`xml.etree._Element`\n+ """\n+ for out_child in outputs_root:\n+ try:\n+ getattr(self, \'_load_{}\'.format(out_child.tag))(root, out_child)\n+ except AttributeError:\n+ logger.warning(out_child.tag + " tag is not processed for <outputs>.")\n+\n+\n+class TestsParser(object):\n+ """\n+ Class to parse content of the <tests> tag from a Galaxy XML wrapper.\n+ """\n+\n+ def _load_param(self, test_root, param_root):\n+ """\n+ Add <param> to the <test>.\n+\n+ :param root: <test> root to append <param> to.\n+ :param repeat_root: root of <param> tag.\n+ :param repeat_root: :class:`xml.etree._Element`\n+ """\n+ test_root.append(gxtp.TestParam(param_root.attrib[\'name\'],\n+ value=param_root.attrib.get(\'value\', None),\n+ ftype=param_root.attrib.get(\'ftype\', None),\n+ dbkey=param_root.attrib.get(\'dbkey\', None)))\n+\n+ def _load_output(self, test_root, output_root):\n+ """\n+ Add <output> to the <test>.\n+\n+ :param root: <test> root to append <output> to.\n+ :param repeat_root: root of <output> tag.\n+ :param repeat_root: :class:`xml.etree._Element`\n+ """\n+ test_root.append(gxtp.TestOutput(name=output_root.attrib.get(\'name\', None),\n+ file=output_root.attrib.get(\'file\', None),\n+ ftype=output_root.attrib.get(\'ftype\', None),\n+ sort=output_root.attrib.get(\'sort\', None),\n+ value=output_root.attrib.get(\'value\', None),\n+ md5=output_root.attrib.get(\'md5\', None),\n+ checksum=output_root.attrib.get(\'checksum\', None),\n+ compare=output_root.attrib.get(\'compare\', None),\n+ lines_diff=output_root.attrib.get(\'lines_diff\', None),\n+ delta=output_root.attrib.get(\'delta\', None)))\n+\n+ def load_tests(self, root, tests_root):\n+ """\n+ Add <tests> to the root.\n+\n+ :param root: root to attach <tests> to (<tool>).\n+ :param tests_root: root of <tests> tag.\n+ :type tests_root: :class:`xml.etree._Element`\n+ """\n+ for test_root in tests_root:\n+ test = gxtp.Test()\n+ for test_child in test_root:\n+ try:\n+ getattr(self, \'_load_{}\'.format(test_child.tag))(test, test_child)\n+ except AttributeError:\n+ logger.warning(test_child.tag + " tag is not processed within <test>.")\n+ root.append(test)\n' |
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| diff -r 5052ac89c036 -r 5d38cb3d9be8 toolfactory/galaxyxml/tool/parameters/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/tool/parameters/__init__.py Sat Aug 08 19:55:55 2020 -0400 |
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| b'@@ -0,0 +1,688 @@\n+from builtins import str\n+from builtins import object\n+from lxml import etree\n+from galaxyxml import Util\n+\n+\n+class XMLParam(object):\n+ name = \'node\'\n+\n+ def __init__(self, *args, **kwargs):\n+ # http://stackoverflow.com/a/12118700\n+ self.children = []\n+ kwargs = {k: v for k, v in list(kwargs.items()) if v is not None}\n+ kwargs = Util.coerce(kwargs, kill_lists=True)\n+ kwargs = Util.clean_kwargs(kwargs, final=True)\n+ self.node = etree.Element(self.name, **kwargs)\n+\n+ def append(self, sub_node):\n+ if self.acceptable_child(sub_node):\n+ # If one of ours, they aren\'t etree nodes, they\'re custom objects\n+ if issubclass(type(sub_node), XMLParam):\n+ self.node.append(sub_node.node)\n+ self.children.append(sub_node)\n+ else:\n+ raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % (\n+ type(self), type(sub_node)))\n+ else:\n+ raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % (\n+ type(self), type(sub_node)))\n+\n+ def validate(self):\n+ # Very few need validation, but some nodes we may want to have\n+ # validation routines on. Should only be called when DONE.\n+ for child in self.children:\n+ # If any child fails to validate return false.\n+ if not child.validate():\n+ return False\n+ return True\n+\n+ def cli(self):\n+ lines = []\n+ for child in self.children:\n+ lines.append(child.command_line())\n+ # lines += child.command_line()\n+ return \'\\n\'.join(lines)\n+\n+ def command_line(self):\n+ return None\n+\n+\n+class RequestParamTranslation(XMLParam):\n+ name = \'request_param_translation\'\n+\n+ def __init__(self, **kwargs):\n+ self.node = etree.Element(self.name)\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, RequestParamTranslation)\n+\n+\n+class RequestParam(XMLParam):\n+ name = \'request_param\'\n+\n+ def __init__(self, galaxy_name, remote_name, missing, **kwargs):\n+ # TODO: bulk copy locals into self.attr?\n+ self.galaxy_name = galaxy_name\n+ # http://stackoverflow.com/a/1408860\n+ params = Util.clean_kwargs(locals().copy())\n+ super(RequestParam, self).__init__(**params)\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, AppendParam) and self.galaxy_name == "URL"\n+\n+\n+class AppendParam(XMLParam):\n+ name = \'append_param\'\n+\n+ def __init__(self, separator="&", first_separator="?", join="=", **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(AppendParam, self).__init__(**params)\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, AppendParamValue)\n+\n+\n+class AppendParamValue(XMLParam):\n+ name = \'value\'\n+\n+ def __init__(self, name="_export", missing="1", **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(AppendParamValue, self).__init__(**params)\n+\n+ def acceptable_child(self, child):\n+ return False\n+\n+\n+class EdamOperations(XMLParam):\n+ name = \'edam_operations\'\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(child), EdamOperation)\n+\n+ def has_operation(self, edam_operation):\n+ """\n+ Check the presence of a given edam_operation.\n+\n+ :type edam_operation: STRING\n+ """\n+ for operation in self.children:\n+ if operation.node.text == edam_operation:\n+ return True\n+ return False\n+\n+\n+class EdamOperation(XMLParam):\n+ name = \'edam_operation\'\n+\n+ def __init__(self, value):\n+ super(EdamOperation, self).__init__()\n+ self.node.text = str(value)\n+\n+\n+class EdamTopics(XMLParam):\n+ name = \'edam_topics\'\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(ch'..b')\n+\n+ def command_line(self):\n+ if hasattr(self, \'command_line_override\'):\n+ return self.command_line_override\n+ else:\n+ return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name())\n+\n+ def mako_name(self):\n+ return \'$\' + self.mako_identifier\n+\n+ def flag(self):\n+ flag = \'-\' * self.num_dashes\n+ return flag + self.mako_identifier\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, OutputFilter) or \\\n+ isinstance(child, ChangeFormat) or \\\n+ isinstance(child, DiscoverDatasets)\n+\n+\n+class OutputFilter(XMLParam):\n+ name = \'filter\'\n+\n+ def __init__(self, text, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ del params[\'text\']\n+ super(OutputFilter, self).__init__(**params)\n+ self.node.text = text\n+\n+ def acceptable_child(self, child):\n+ return False\n+\n+\n+class ChangeFormat(XMLParam):\n+ name = \'change_format\'\n+\n+ def __init__(self, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(ChangeFormat, self).__init__(**params)\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, ChangeFormatWhen)\n+\n+\n+class ChangeFormatWhen(XMLParam):\n+ name = \'when\'\n+\n+ def __init__(self, input, format, value, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(ChangeFormatWhen, self).__init__(**params)\n+\n+ def acceptable_child(self, child):\n+ return False\n+\n+\n+class OutputCollection(XMLParam):\n+ name = \'collection\'\n+\n+ def __init__(self, name, type=None, label=None, format_source=None,\n+ type_source=None, structured_like=None, inherit_format=None, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(OutputCollection, self).__init__(**params)\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, OutputData) or isinstance(child, OutputFilter) \\\n+ or isinstance(child, DiscoverDatasets)\n+\n+\n+class DiscoverDatasets(XMLParam):\n+ name = \'discover_datasets\'\n+\n+ def __init__(self, pattern, directory=None, format=None, ext=None,\n+ visible=None, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(DiscoverDatasets, self).__init__(**params)\n+\n+\n+class Tests(XMLParam):\n+ name = \'tests\'\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(child), Test)\n+\n+\n+class Test(XMLParam):\n+ name = \'test\'\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, TestParam) or isinstance(child, TestOutput)\n+\n+\n+class TestParam(XMLParam):\n+ name = \'param\'\n+\n+ def __init__(self, name, value=None, ftype=None, dbkey=None, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(TestParam, self).__init__(**params)\n+\n+\n+class TestOutput(XMLParam):\n+ name = \'output\'\n+\n+ def __init__(self, name=None, file=None, ftype=None, sort=None, value=None,\n+ md5=None, checksum=None, compare=None, lines_diff=None,\n+ delta=None, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(TestOutput, self).__init__(**params)\n+\n+\n+class Citations(XMLParam):\n+ name = \'citations\'\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(child), Citation)\n+\n+ def has_citation(self, type, value):\n+ """\n+ Check the presence of a given citation.\n+\n+ :type type: STRING\n+ :type value: STRING\n+ """\n+ for citation in self.children:\n+ if citation.node.attrib[\'type\'] == type and citation.node.text == value:\n+ return True\n+ return False\n+\n+\n+class Citation(XMLParam):\n+ name = \'citation\'\n+\n+ def __init__(self, type, value):\n+ passed_kwargs = {}\n+ passed_kwargs[\'type\'] = type\n+ super(Citation, self).__init__(**passed_kwargs)\n+ self.node.text = str(value)\n' |
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| diff -r 5052ac89c036 -r 5d38cb3d9be8 toolfactory/sample_toolfactory_tools.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/sample_toolfactory_tools.ga Sat Aug 08 19:55:55 2020 -0400 |
| [ |
| b'@@ -0,0 +1,443 @@\n+{\n+ "a_galaxy_workflow": "true",\n+ "annotation": "",\n+ "format-version": "0.1",\n+ "name": "workflow to generate a bunch of sample toolfactory tools",\n+ "steps": {\n+ "0": {\n+ "annotation": "",\n+ "content_id": null,\n+ "errors": null,\n+ "id": 0,\n+ "input_connections": {},\n+ "inputs": [\n+ {\n+ "description": "",\n+ "name": "rgToolFactory2.py"\n+ }\n+ ],\n+ "label": "rgToolFactory2.py",\n+ "name": "Input dataset",\n+ "outputs": [],\n+ "position": {\n+ "bottom": 235.25,\n+ "height": 81,\n+ "left": 711.84375,\n+ "right": 911.84375,\n+ "top": 154.25,\n+ "width": 200,\n+ "x": 711.84375,\n+ "y": 154.25\n+ },\n+ "tool_id": null,\n+ "tool_state": "{\\"optional\\": false}",\n+ "tool_version": null,\n+ "type": "data_input",\n+ "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666",\n+ "workflow_outputs": [\n+ {\n+ "label": null,\n+ "output_name": "output",\n+ "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89"\n+ }\n+ ]\n+ },\n+ "1": {\n+ "annotation": "",\n+ "content_id": null,\n+ "errors": null,\n+ "id": 1,\n+ "input_connections": {},\n+ "inputs": [\n+ {\n+ "description": "",\n+ "name": "README.md"\n+ }\n+ ],\n+ "label": "README.md",\n+ "name": "Input dataset",\n+ "outputs": [],\n+ "position": {\n+ "bottom": 760.25,\n+ "height": 61,\n+ "left": 711.84375,\n+ "right": 911.84375,\n+ "top": 699.25,\n+ "width": 200,\n+ "x": 711.84375,\n+ "y": 699.25\n+ },\n+ "tool_id": null,\n+ "tool_state": "{\\"optional\\": false}",\n+ "tool_version": null,\n+ "type": "data_input",\n+ "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27",\n+ "workflow_outputs": [\n+ {\n+ "label": null,\n+ "output_name": "output",\n+ "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095"\n+ }\n+ ]\n+ },\n+ "2": {\n+ "annotation": "",\n+ "content_id": null,\n+ "errors": null,\n+ "id": 2,\n+ "input_connections": {},\n+ "inputs": [\n+ {\n+ "description": "",\n+ "name": "testtext"\n+ }\n+ ],\n+ "label": "testtext",\n+ "name": "Input dataset",\n+ "outputs": [],\n+ "position": {\n+ "bottom": 235.25,\n+ 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\\"interpreter_version\\": \\"\\", \\"exe_package_version\\": \\"\\", \\"dynScript\\": \\"import argparse\\\\nimport tarfile\\\\nimport os\\\\nimport tempfile\\\\nimport subprocess\\\\n\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\n\\\\nparser = argparse.ArgumentParser()\\\\na = parser.add_argument\\\\na(\'--tooltgz\',default=\'\')\\\\na(\'--report\',default=None)\\\\na(\'--toolout\',default=None)\\\\na(\'--galaxy_root\',default=None)\\\\nargs = parser.parse_args()\\\\ntoolname = args.toolout.split(os.sep)[-1]\\\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\\\ntf = tarfile.open(args.tooltgz,\\\\\\"r:gz\\\\\\")\\\\ntf.extractall(toolpath)\\\\ncl = \\\\\\"planemo test --skip_venv --galaxy_root %s %s\\\\\\" % (args.galaxy_root,toolpath)\\\\ncll = cl.split(\' \')\\\\nsto = open(args.report, \'w\')\\\\np = 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\\"history_outputs\\": [{\\"__index__\\": 0, \\"history_name\\": \\"report\\", \\"history_format\\": \\"txt\\", \\"history_CL\\": \\"report\\"}], \\"edit_params\\": \\"yes\\", \\"additional_parameters\\": [{\\"__index__\\": 0, \\"param_name\\": \\"toolout\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"tools/toolmakers/planemotest\\", \\"param_label\\": \\"output path under galaxy root\\", \\"param_help\\": \\"This is where the tgz file will be extracted and tested by planemo\\", \\"param_CL\\": \\"toolout\\"}, {\\"__index__\\": 1, \\"param_name\\": \\"galaxy_root\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"/home/ross/galaxy\\", \\"param_label\\": \\"your galaxy root to use for running planemo\\", \\"param_help\\": \\"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\\", \\"param_CL\\": \\"galaxy_root\\"}]}, \\"tool_name\\": \\"planemotest\\", 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