Galaxy |

Changeset 36:ce2b1f8ea68d (2020-08-10)

Previous changeset 35:5d38cb3d9be8 (2020-08-08) Next changeset 37:099047ee7094 (2020-08-10)

Commit message:
passes flake8 tests finally :)

modified:
toolfactory/galaxyxml/__init__.py
toolfactory/galaxyxml/tool/__init__.py
toolfactory/galaxyxml/tool/import_xml.py
toolfactory/galaxyxml/tool/parameters/__init__.py
toolfactory/rgToolFactory2.py
toolfactory/rgToolFactory2.xml

added:
toolfactory/sample_toolfactory_tools.tgz
toolfactory/tf_tests_history.tar.gz
toolfactory/tfwfsample.tgz
toolfactory/tfworkflowsample.ga

removed:
toolfactory/sample_toolfactory_tools.ga

diff -r 5d38cb3d9be8 -r ce2b1f8ea68d toolfactory/galaxyxml/__init__.py
--- a/toolfactory/galaxyxml/__init__.py Sat Aug 08 19:55:55 2020 -0400
+++ b/toolfactory/galaxyxml/__init__.py Mon Aug 10 23:24:41 2020 -0400

[

@@ -4,23 +4,24 @@

class GalaxyXML(object):
-
     def __init__(self):
-        self.root = etree.Element('root')
+        self.root = etree.Element("root")

     def export(self):
-        return etree.tostring(self.root, pretty_print=True, encoding='unicode')
+        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}
+            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])
@@ -45,22 +46,22 @@

     @classmethod
     def clean_kwargs(cls, params, final=False):
-        if 'kwargs' in params:
-            kwargs = params['kwargs']
+        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']
+            del params["kwargs"]
+        if "self" in params:
+            del params["self"]

-        if '__class__' in params:
-            del params['__class__']
+        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',):
+            for blacklist in ("positional",):
                 if blacklist in params:
                     del params[blacklist]
         return params

diff -r 5d38cb3d9be8 -r ce2b1f8ea68d toolfactory/galaxyxml/tool/__init__.py
--- a/toolfactory/galaxyxml/tool/__init__.py Sat Aug 08 19:55:55 2020 -0400
+++ b/toolfactory/galaxyxml/tool/__init__.py Mon Aug 10 23:24:41 2020 -0400

[

@@ -4,56 +4,68 @@
from galaxyxml import Util, GalaxyXML
from galaxyxml.tool.parameters import XMLParam

-VALID_TOOL_TYPES = ('data_source', 'data_source_async')
-VALID_URL_METHODS = ('get', 'post')
+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):
+    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,
+            "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']
+            del kwargs["hidden"]
         if workflow_compatible:
-            del kwargs['workflow_compatible']
+            del kwargs["workflow_compatible"]

         kwargs = Util.coerce(kwargs)
-        self.root = etree.Element('tool', **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))
+                raise Exception(
+                    "Tool type must be one of %s" % ",".join(VALID_TOOL_TYPES)
+                )
             else:
-                kwargs['tool_type'] = tool_type
+                kwargs["tool_type"] = tool_type

                 if URL_method is not None:
                     if URL_method in VALID_URL_METHODS:
-                        kwargs['URL_method'] = URL_method
+                        kwargs["URL_method"] = URL_method
                     else:
-                        raise Exception("URL_method must be one of %s" %
-                                        ','.join(VALID_URL_METHODS))
+                        raise Exception(
+                            "URL_method must be one of %s" % ",".join(VALID_URL_METHODS)
+                        )

-        description_node = etree.SubElement(self.root, 'description')
+        description_node = etree.SubElement(self.root, "description")
         description_node.text = description

     def add_comment(self, comment_txt):
@@ -61,7 +73,7 @@
         self.root.insert(0, comment)

     def append_version_command(self):
-        version_command = etree.SubElement(self.root, 'version_command')
+        version_command = etree.SubElement(self.root, "version_command")
         try:
             version_command.text = etree.CDATA(self.version_command)
         except Exception:
@@ -76,10 +88,10 @@
     def clean_command_string(self, command_line):
         clean = []
         for x in command_line:
-            if x is not [] and x is not ['']:
+            if x is not [] and x is not [""]:
                 clean.append(x)

-        return '\n'.join(clean)
+        return "\n".join(clean)

     def export(self, keep_old_command=False):  # noqa

@@ -105,7 +117,7 @@
         except Exception:
             pass

-        if self.command_line_override != None:
+        if self.command_line_override:
             command_line = self.command_line_override
         else:
             command_line = []
@@ -120,8 +132,8 @@
                 pass

         # Add stdio section
-        stdio = etree.SubElement(export_xml.root, 'stdio')
-        etree.SubElement(stdio, 'exit_code', range='1:', level='fatal')
+        stdio = etree.SubElement(export_xml.root, "stdio")
+        etree.SubElement(stdio, "exit_code", range="1:", level="fatal")

         # Append version command
         export_xml.append_version_command()
@@ -129,21 +141,25 @@
         # Steal interpreter from kwargs
         command_kwargs = {}
         if export_xml.interpreter is not None:
-            command_kwargs['interpreter'] = export_xml.interpreter
+            command_kwargs["interpreter"] = export_xml.interpreter

         # Add command section
-        command_node = etree.SubElement(export_xml.root, 'command', **command_kwargs)
+        command_node = etree.SubElement(export_xml.root, "command", **command_kwargs)

         if keep_old_command:
-            if getattr(self, 'command', None):
+            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.')
+                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))
+                export_xml.executable,
+                export_xml.clean_command_string(command_line),
+            )
             command_node.text = etree.CDATA(actual_cli.strip())

         try:
@@ -161,7 +177,7 @@
         except Exception:
             pass

-        help_element = etree.SubElement(export_xml.root, 'help')
+        help_element = etree.SubElement(export_xml.root, "help")
         help_element.text = etree.CDATA(export_xml.help)

         try:

diff -r 5d38cb3d9be8 -r ce2b1f8ea68d toolfactory/galaxyxml/tool/import_xml.py
--- a/toolfactory/galaxyxml/tool/import_xml.py Sat Aug 08 19:55:55 2020 -0400
+++ b/toolfactory/galaxyxml/tool/import_xml.py Mon Aug 10 23:24:41 2020 -0400

[

b'@@ -22,24 +22,26 @@\n version_cmd = None\n description = None\n for child in xml_root:\n- if child.tag == \'description\':\n+ if child.tag == "description":\n description = child.text\n- elif child.tag == \'command\':\n+ elif child.tag == "command":\n executable = child.text.split()[0]\n command = child.text\n- elif child.tag == \'version_command\':\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 = gxt.Tool(\n+ 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+ )\n tool.command = command\n return tool\n \n@@ -109,15 +111,17 @@\n """\n tool.requirements = gxtp.Requirements()\n for req in requirements_root:\n- req_type = req.attrib[\'type\']\n+ req_type = req.attrib["type"]\n value = req.text\n- if req.tag == \'requirement\':\n- version = req.attrib.get(\'version\', None)\n- tool.requirements.append(gxtp.Requirement(req_type, value, version=version))\n- elif req.tag == \'container\':\n+ if req.tag == "requirement":\n+ version = req.attrib.get("version", None)\n+ tool.requirements.append(\n+ gxtp.Requirement(req_type, value, version=version)\n+ )\n+ elif req.tag == "container":\n tool.requirements.append(gxtp.Container(req_type, value))\n else:\n- logger.warning(req.tag + \' is not a valid tag for requirements child\')\n+ logger.warning(req.tag + " is not a valid tag for requirements child")\n \n def _load_edam_topics(self, tool, topics_root):\n """\n@@ -156,7 +160,7 @@\n """\n tool.configfiles = gxtp.Configfiles()\n for conf in configfiles_root:\n- name = conf.attrib[\'name\']\n+ name = conf.attrib["name"]\n value = conf.text\n tool.configfiles.append(gxtp.Configfile(name, value))\n \n@@ -171,7 +175,7 @@\n """\n tool.citations = gxtp.Citations()\n for cit in citations_root:\n- cit_type = cit.attrib[\'type\']\n+ cit_type = cit.attrib["type"]\n value = cit.text\n tool.citations.append(gxtp.Citation(cit_type, value))\n \n@@ -228,7 +232,7 @@\n # Now we import each tag\'s field\n for child in xml_root:\n try:\n- getattr(self, \'_load_{}\'.format(child.tag))(tool, child)\n+ getattr(self, "_load_{}".format(child.tag))(tool, child)\n except AttributeError:\n logger.warning(child.tag + " tag is not processed.")\n return tool\n@@ -247,11 +251,15 @@\n :param text_param: root of <param> tag.\n :type text_param: :class:`xml.etree._Element`\n """\n- root.append(gxtp.TextParam(text_par'..b' 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+ )\n \n def _load_filter(self, root, filter_root):\n """\n@@ -600,7 +661,7 @@\n """\n for out_child in outputs_root:\n try:\n- getattr(self, \'_load_{}\'.format(out_child.tag))(root, out_child)\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@@ -618,10 +679,14 @@\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+ test_root.append(\n+ gxtp.TestParam(\n+ 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+ )\n \n def _load_output(self, test_root, output_root):\n """\n@@ -631,16 +696,20 @@\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+ test_root.append(\n+ gxtp.TestOutput(\n+ 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+ )\n \n def load_tests(self, root, tests_root):\n """\n@@ -654,7 +723,9 @@\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+ 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+ logger.warning(\n+ test_child.tag + " tag is not processed within <test>."\n+ )\n root.append(test)\n'

diff -r 5d38cb3d9be8 -r ce2b1f8ea68d toolfactory/galaxyxml/tool/parameters/__init__.py
--- a/toolfactory/galaxyxml/tool/parameters/__init__.py Sat Aug 08 19:55:55 2020 -0400
+++ b/toolfactory/galaxyxml/tool/parameters/__init__.py Mon Aug 10 23:24:41 2020 -0400

[

b'@@ -5,7 +5,7 @@\n \n \n class XMLParam(object):\n- name = \'node\'\n+ name = "node"\n \n def __init__(self, *args, **kwargs):\n # http://stackoverflow.com/a/12118700\n@@ -22,11 +22,15 @@\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+ raise Exception(\n+ "Child was unacceptable to parent (%s is not appropriate for %s)"\n+ % (type(self), type(sub_node))\n+ )\n else:\n- raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % (\n- type(self), type(sub_node)))\n+ raise Exception(\n+ "Child was unacceptable to parent (%s is not appropriate for %s)"\n+ % (type(self), type(sub_node))\n+ )\n \n def validate(self):\n # Very few need validation, but some nodes we may want to have\n@@ -42,14 +46,14 @@\n for child in self.children:\n lines.append(child.command_line())\n # lines += child.command_line()\n- return \'\\n\'.join(lines)\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+ name = "request_param_translation"\n \n def __init__(self, **kwargs):\n self.node = etree.Element(self.name)\n@@ -59,7 +63,7 @@\n \n \n class RequestParam(XMLParam):\n- name = \'request_param\'\n+ name = "request_param"\n \n def __init__(self, galaxy_name, remote_name, missing, **kwargs):\n # TODO: bulk copy locals into self.attr?\n@@ -73,7 +77,7 @@\n \n \n class AppendParam(XMLParam):\n- name = \'append_param\'\n+ name = "append_param"\n \n def __init__(self, separator="&", first_separator="?", join="=", **kwargs):\n params = Util.clean_kwargs(locals().copy())\n@@ -84,7 +88,7 @@\n \n \n class AppendParamValue(XMLParam):\n- name = \'value\'\n+ name = "value"\n \n def __init__(self, name="_export", missing="1", **kwargs):\n params = Util.clean_kwargs(locals().copy())\n@@ -95,7 +99,7 @@\n \n \n class EdamOperations(XMLParam):\n- name = \'edam_operations\'\n+ name = "edam_operations"\n \n def acceptable_child(self, child):\n return issubclass(type(child), EdamOperation)\n@@ -113,7 +117,7 @@\n \n \n class EdamOperation(XMLParam):\n- name = \'edam_operation\'\n+ name = "edam_operation"\n \n def __init__(self, value):\n super(EdamOperation, self).__init__()\n@@ -121,7 +125,7 @@\n \n \n class EdamTopics(XMLParam):\n- name = \'edam_topics\'\n+ name = "edam_topics"\n \n def acceptable_child(self, child):\n return issubclass(type(child), EdamTopic)\n@@ -139,7 +143,7 @@\n \n \n class EdamTopic(XMLParam):\n- name = \'edam_topic\'\n+ name = "edam_topic"\n \n def __init__(self, value):\n super(EdamTopic, self).__init__()\n@@ -147,70 +151,81 @@\n \n \n class Requirements(XMLParam):\n- name = \'requirements\'\n+ name = "requirements"\n # This bodes to be an issue -__-\n \n def acceptable_child(self, child):\n- return issubclass(type(child), Requirement) or issubclass(type(child), Container)\n+ return issubclass(type(child), Requirement) or issubclass(\n+ type(child), Container\n+ )\n \n \n class Requirement(XMLParam):\n- name = \'requirement\'\n+ name = "requirement"\n \n def __init__(self, type, value, version=None, **kwargs):\n params = Util.clean_kwargs(locals().copy())\n passed_kwargs = {}\n- passed_kwargs[\'version\'] = params[\'version\']\n- passed_kwargs[\'type\'] = params[\'type\']\n+ passed_kwargs["version"] = params["version"]\n+ passed_kwargs["type"] = params["type"]\n super(Requirement, self).__init__(**passed_kwargs)\n self.node.text = str(value)\n \n \n class Container(XMLPa'..b' params = Util.clean_kwargs(locals().copy())\n- del params[\'text\']\n+ del params["text"]\n super(OutputFilter, self).__init__(**params)\n self.node.text = text\n \n@@ -584,7 +680,7 @@\n \n \n class ChangeFormat(XMLParam):\n- name = \'change_format\'\n+ name = "change_format"\n \n def __init__(self, **kwargs):\n params = Util.clean_kwargs(locals().copy())\n@@ -595,7 +691,7 @@\n \n \n class ChangeFormatWhen(XMLParam):\n- name = \'when\'\n+ name = "when"\n \n def __init__(self, input, format, value, **kwargs):\n params = Util.clean_kwargs(locals().copy())\n@@ -606,43 +702,56 @@\n \n \n class OutputCollection(XMLParam):\n- name = \'collection\'\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+ def __init__(\n+ self,\n+ name,\n+ type=None,\n+ label=None,\n+ format_source=None,\n+ type_source=None,\n+ structured_like=None,\n+ inherit_format=None,\n+ **kwargs,\n+ ):\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+ return (\n+ isinstance(child, OutputData)\n+ or isinstance(child, OutputFilter)\n or isinstance(child, DiscoverDatasets)\n+ )\n \n \n class DiscoverDatasets(XMLParam):\n- name = \'discover_datasets\'\n+ name = "discover_datasets"\n \n- def __init__(self, pattern, directory=None, format=None, ext=None,\n- visible=None, **kwargs):\n+ def __init__(\n+ self, pattern, directory=None, format=None, ext=None, visible=None, **kwargs\n+ ):\n params = Util.clean_kwargs(locals().copy())\n super(DiscoverDatasets, self).__init__(**params)\n \n \n class Tests(XMLParam):\n- name = \'tests\'\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+ 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+ name = "param"\n \n def __init__(self, name, value=None, ftype=None, dbkey=None, **kwargs):\n params = Util.clean_kwargs(locals().copy())\n@@ -650,17 +759,28 @@\n \n \n class TestOutput(XMLParam):\n- name = \'output\'\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+ def __init__(\n+ self,\n+ name=None,\n+ file=None,\n+ ftype=None,\n+ sort=None,\n+ value=None,\n+ md5=None,\n+ checksum=None,\n+ compare=None,\n+ lines_diff=None,\n+ delta=None,\n+ **kwargs,\n+ ):\n params = Util.clean_kwargs(locals().copy())\n super(TestOutput, self).__init__(**params)\n \n \n class Citations(XMLParam):\n- name = \'citations\'\n+ name = "citations"\n \n def acceptable_child(self, child):\n return issubclass(type(child), Citation)\n@@ -673,16 +793,16 @@\n :type value: STRING\n """\n for citation in self.children:\n- if citation.node.attrib[\'type\'] == type and citation.node.text == value:\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+ name = "citation"\n \n def __init__(self, type, value):\n passed_kwargs = {}\n- passed_kwargs[\'type\'] = type\n+ passed_kwargs["type"] = type\n super(Citation, self).__init__(**passed_kwargs)\n self.node.text = str(value)\n'

diff -r 5d38cb3d9be8 -r ce2b1f8ea68d toolfactory/rgToolFactory2.py
--- a/toolfactory/rgToolFactory2.py Sat Aug 08 19:55:55 2020 -0400
+++ b/toolfactory/rgToolFactory2.py Mon Aug 10 23:24:41 2020 -0400

[

b'@@ -19,27 +19,30 @@\n # TODO: add option to run that code as a post execution hook\n # TODO: add additional history input parameters - currently only one\n \n-import sys\n+\n+import argparse\n+import logging\n+import os\n+import re\n+import shutil\n import subprocess\n-import shutil\n-import os\n+import sys\n+import tarfile\n+import tempfile\n import time\n-import tempfile\n-import argparse\n-import tarfile\n-import re\n+\n import galaxyxml.tool as gxt\n import galaxyxml.tool.parameters as gxtp\n-import logging\n+import lxml\n \n-\n+foo = lxml.__name__ # fug you, flake8. Say my name! Please accept the PR, Helena!\n \n progname = os.path.split(sys.argv[0])[1]\n-myversion = \'V2.1 July 2020\'\n+myversion = "V2.1 July 2020"\n verbose = True\n debug = True\n-toolFactoryURL = \'https://github.com/fubar2/toolfactory\'\n-ourdelim = \'~~~\'\n+toolFactoryURL = "https://github.com/fubar2/toolfactory"\n+ourdelim = "~~~"\n \n # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label~~~$input_help"\n IPATHPOS = 0\n@@ -54,7 +57,7 @@\n OCLPOS = 2\n OOCLPOS = 3\n \n-#--additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL"\n+# --additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL"\n ANAMEPOS = 0\n AVALPOS = 1\n ALABPOS = 2\n@@ -63,10 +66,11 @@\n ACLPOS = 5\n AOCLPOS = 6\n \n+\n def timenow():\n """return current time as a string\n """\n- return time.strftime(\'%d/%m/%Y %H:%M:%S\', time.localtime(time.time()))\n+ return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))\n \n \n def quote_non_numeric(s):\n@@ -80,12 +84,7 @@\n return \'"%s"\' % s\n \n \n-html_escape_table = {\n- "&": "&",\n- ">": ">",\n- "<": "<",\n- "$": r"\\$"\n-}\n+html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\\$"}\n \n \n def html_escape(text):\n@@ -95,10 +94,10 @@\n \n def html_unescape(text):\n """Revert entities within text. Multiple character targets so use replace"""\n- t = text.replace(\'&\', \'&\')\n- t = t.replace(\'>\', \'>\')\n- t = t.replace(\'<\', \'<\')\n- t = t.replace(\'\\\\$\', \'$\')\n+ t = text.replace("&", "&")\n+ t = t.replace(">", ">")\n+ t = t.replace("<", "<")\n+ t = t.replace("\\\\$", "$")\n return t\n \n \n@@ -111,8 +110,7 @@\n if citation.startswith("doi"):\n citation_tuples.append(("doi", citation[len("doi"):].strip()))\n else:\n- citation_tuples.append(\n- ("bibtex", citation[len("bibtex"):].strip()))\n+ citation_tuples.append(("bibtex", citation[len("bibtex"):].strip()))\n return citation_tuples\n \n \n@@ -121,8 +119,7 @@\n uses galaxyxml\n \n """\n- \n- \n+\n def __init__(self, args=None):\n """\n prepare command line cl for running the tool here\n@@ -138,38 +135,43 @@\n self.lastxclredirect = None\n self.cl = []\n self.xmlcl = []\n+ self.is_positional = self.args.parampass == "positional"\n aCL = self.cl.append\n- assert args.parampass in [\'0\',\'argparse\',\'positional\'],\'Parameter passing in args.parampass must be "0","positional" or "argparse"\'\n- self.tool_name = re.sub(\'[^a-zA-Z0-9_]+\', \'\', args.tool_name)\n+ assert args.parampass in [\n+ "0",\n+ "argparse",\n+ "positional",\n+ ], \'Parameter passing in args.parampass must be "0","positional" or "argparse"\'\n+ self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)\n self.tool_id = self.tool_name\n- self.xmlfile = \'%s.xml\' % self.tool_name\n- if self.args.runmode == "Executable" or self.args.runmode == "system": # binary - no need\n+ self.xmlfile = "%s.xml" % self.tool_name\n+ if self.args.interpreter_name:\n+ exe = "$runMe"\n+ else:\n+ exe = self.args.exe_package\n+ assert (\n+ exe is not None\n+ ), "No interpeter or executable passed in - nothing to run so cannot build"\n+ self.tool = gxt.Tool(\n+'..b'\n- logging.debug(\'run done\')\n+ logging.debug("run done")\n return retval\n \n \n@@ -567,40 +628,43 @@\n """\n parser = argparse.ArgumentParser()\n a = parser.add_argument\n- a(\'--script_path\', default=\'\')\n- a(\'--tool_name\', default=None)\n- a(\'--interpreter_name\', default=None)\n- a(\'--interpreter_version\', default=None)\n- a(\'--exe_package\', default=None)\n- a(\'--exe_package_version\', default=None)\n- a(\'--input_files\', default=[], action="append")\n- a(\'--output_files\', default=[], action="append")\n- a(\'--user_email\', default=\'Unknown\')\n- a(\'--bad_user\', default=None)\n- a(\'--make_Tool\', default=None)\n- a(\'--help_text\', default=None)\n- a(\'--tool_desc\', default=None)\n- a(\'--tool_version\', default=None)\n- a(\'--citations\', default=None)\n- a(\'--additional_parameters\', action=\'append\', default=[])\n- a(\'--edit_additional_parameters\', action="store_true", default=False)\n- a(\'--parampass\', default="positional")\n- a(\'--tfout\', default="./tfout")\n- a(\'--new_tool\',default="new_tool")\n- a(\'--runmode\',default=None)\n+ a("--script_path", default="")\n+ a("--tool_name", default=None)\n+ a("--interpreter_name", default=None)\n+ a("--interpreter_version", default=None)\n+ a("--exe_package", default=None)\n+ a("--exe_package_version", default=None)\n+ a("--input_files", default=[], action="append")\n+ a("--output_files", default=[], action="append")\n+ a("--user_email", default="Unknown")\n+ a("--bad_user", default=None)\n+ a("--make_Tool", default=None)\n+ a("--help_text", default=None)\n+ a("--tool_desc", default=None)\n+ a("--tool_version", default=None)\n+ a("--citations", default=None)\n+ a("--additional_parameters", action="append", default=[])\n+ a("--edit_additional_parameters", action="store_true", default=False)\n+ a("--parampass", default="positional")\n+ a("--tfout", default="./tfout")\n+ a("--new_tool", default="new_tool")\n+ a("--runmode", default=None)\n args = parser.parse_args()\n- assert not args.bad_user, \'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file\' % (\n- args.bad_user, args.bad_user)\n- assert args.tool_name, \'## Tool Factory expects a tool name - eg --tool_name=DESeq\'\n- assert (args.interpreter_name or args.exe_package), \'## Tool Factory wrapper expects an interpreter - eg --interpreter_name=Rscript or an executable package findable by the dependency management package\'\n- assert args.exe_package or (len(args.script_path) > 0 and os.path.isfile(\n- args.script_path)), \'## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable\'\n- args.input_files = [x.replace(\'"\', \'\').replace("\'", \'\')\n- for x in args.input_files]\n+ assert not args.bad_user, (\n+ \'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file\'\n+ % (args.bad_user, args.bad_user)\n+ )\n+ assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"\n+ assert (\n+ args.interpreter_name or args.exe_package\n+ ), "## Tool Factory wrapper expects an interpreter or an executable package"\n+ assert args.exe_package or (\n+ len(args.script_path) > 0 and os.path.isfile(args.script_path)\n+ ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable"\n+ args.input_files = [x.replace(\'"\', "").replace("\'", "") for x in args.input_files]\n # remove quotes we need to deal with spaces in CL params\n for i, x in enumerate(args.additional_parameters):\n- args.additional_parameters[i] = args.additional_parameters[i].replace(\n- \'"\', \'\')\n+ args.additional_parameters[i] = args.additional_parameters[i].replace(\'"\', "")\n r = ScriptRunner(args)\n if args.make_Tool:\n retcode = r.makeTooltar()\n'

diff -r 5d38cb3d9be8 -r ce2b1f8ea68d toolfactory/rgToolFactory2.xml
--- a/toolfactory/rgToolFactory2.xml Sat Aug 08 19:55:55 2020 -0400
+++ b/toolfactory/rgToolFactory2.xml Mon Aug 10 23:24:41 2020 -0400

[

@@ -122,6 +122,7 @@
   </macros>
    <requirements>
       <requirement type="package">python</requirement>
+      <requirement type="package">lxml</requirement>
   </requirements>
   <command interpreter="python"><![CDATA[
#import os

diff -r 5d38cb3d9be8 -r ce2b1f8ea68d toolfactory/sample_toolfactory_tools.ga
--- a/toolfactory/sample_toolfactory_tools.ga Sat Aug 08 19:55:55 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,443 +0,0 @@\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- "height": 61,\n- "left": 989.84375,\n- "right": 1189.84375,\n- "top": 174.25,\n- "width": 200,\n- "x": 989.84375,\n- "y": 174.25\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa"\n- }\n- ]\n- },\n- "3": {\n- "annotation": "",\n- "content_id": "rgTF2",\n- "errors": null,\n- "id": 3,\n- "input_connections": {\n- '..b'\n- "bottom": 1271.25,\n- "height": 242,\n- "left": 1267.84375,\n- "right": 1467.84375,\n- "top": 1029.25,\n- "width": 200,\n- "x": 1267.84375,\n- "y": 1029.25\n- },\n- "post_job_actions": {},\n- "tool_id": "rgTF2",\n- "tool_state": "{\\"__input_ext\\": \\"tgz\\", \\"chromInfo\\": \\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\\", \\"interexe\\": {\\"interpreter\\": \\"python\\", \\"__current_case__\\": 2, \\"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 = subprocess.run(cll, shell=False, stdout=sto)\\\\nretval = p.returncode\\\\nsto.close()\\\\n\\"}, \\"makeMode\\": {\\"make_Tool\\": \\"yes\\", \\"__current_case__\\": 0, \\"tool_version\\": \\"0.01\\", \\"tool_desc\\": \\"Tool to test toolshed tool archives generated by the tool factory.\\", \\"help_text\\": \\"**What it Does**\\\\n\\\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\\\nIt was generated using the tool factory.\\", \\"citations\\": []}, \\"ppass\\": {\\"parampass\\": \\"argparse\\", \\"__current_case__\\": 0, \\"history_inputs\\": [{\\"__index__\\": 0, \\"input_files\\": {\\"__class__\\": \\"ConnectedValue\\"}, \\"input_formats\\": [\\"tgz\\"], \\"input_label\\": \\"tool toolshed tgz archive from history\\", \\"input_help\\": \\"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\\", \\"input_CL\\": \\"tooltgz\\"}], \\"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\\", \\"__page__\\": null, \\"__rerun_remap_job_id__\\": null}",\n- "tool_version": "2.00",\n- "type": "tool",\n- "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "ToolFactory_Outputs",\n- "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027"\n- },\n- {\n- "label": null,\n- "output_name": "new_tool",\n- "uuid": "744499de-5d7e-4415-b427-315057c81ebc"\n- }\n- ]\n- }\n- },\n- "tags": [],\n- "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b",\n- "version": 1\n-}\n'

diff -r 5d38cb3d9be8 -r ce2b1f8ea68d toolfactory/sample_toolfactory_tools.tgz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/sample_toolfactory_tools.tgz Mon Aug 10 23:24:41 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+ "height": 61,\n+ "left": 989.84375,\n+ "right": 1189.84375,\n+ "top": 174.25,\n+ "width": 200,\n+ "x": 989.84375,\n+ "y": 174.25\n+ },\n+ "tool_id": null,\n+ "tool_state": "{\\"optional\\": false}",\n+ "tool_version": null,\n+ "type": "data_input",\n+ "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9",\n+ "workflow_outputs": [\n+ {\n+ "label": null,\n+ "output_name": "output",\n+ "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa"\n+ }\n+ ]\n+ },\n+ "3": {\n+ "annotation": "",\n+ "content_id": "rgTF2",\n+ "errors": null,\n+ "id": 3,\n+ "input_connections": {\n+ '..b'\n+ "bottom": 1271.25,\n+ "height": 242,\n+ "left": 1267.84375,\n+ "right": 1467.84375,\n+ "top": 1029.25,\n+ "width": 200,\n+ "x": 1267.84375,\n+ "y": 1029.25\n+ },\n+ "post_job_actions": {},\n+ "tool_id": "rgTF2",\n+ "tool_state": "{\\"__input_ext\\": \\"tgz\\", \\"chromInfo\\": \\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\\", \\"interexe\\": {\\"interpreter\\": \\"python\\", \\"__current_case__\\": 2, \\"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 = subprocess.run(cll, shell=False, stdout=sto)\\\\nretval = p.returncode\\\\nsto.close()\\\\n\\"}, \\"makeMode\\": {\\"make_Tool\\": \\"yes\\", \\"__current_case__\\": 0, \\"tool_version\\": \\"0.01\\", \\"tool_desc\\": \\"Tool to test toolshed tool archives generated by the tool factory.\\", \\"help_text\\": \\"**What it Does**\\\\n\\\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\\\nIt was generated using the tool factory.\\", \\"citations\\": []}, \\"ppass\\": {\\"parampass\\": \\"argparse\\", \\"__current_case__\\": 0, \\"history_inputs\\": [{\\"__index__\\": 0, \\"input_files\\": {\\"__class__\\": \\"ConnectedValue\\"}, \\"input_formats\\": [\\"tgz\\"], \\"input_label\\": \\"tool toolshed tgz archive from history\\", \\"input_help\\": \\"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\\", \\"input_CL\\": \\"tooltgz\\"}], \\"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\\", \\"__page__\\": null, \\"__rerun_remap_job_id__\\": null}",\n+ "tool_version": "2.00",\n+ "type": "tool",\n+ "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd",\n+ "workflow_outputs": [\n+ {\n+ "label": null,\n+ "output_name": "ToolFactory_Outputs",\n+ "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027"\n+ },\n+ {\n+ "label": null,\n+ "output_name": "new_tool",\n+ "uuid": "744499de-5d7e-4415-b427-315057c81ebc"\n+ }\n+ ]\n+ }\n+ },\n+ "tags": [],\n+ "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b",\n+ "version": 1\n+}\n'

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[