| Previous changeset 38:a30536c100bf (2020-08-12) Next changeset 40:51fa77152988 (2020-08-13) |
|
Commit message:
Uploaded |
|
modified:
toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
|
removed:
toolfactory/__init__.py toolfactory/galaxyxml/__init__.py toolfactory/galaxyxml/__pycache__/__init__.cpython-36.pyc toolfactory/galaxyxml/tool/__init__.py toolfactory/galaxyxml/tool/__pycache__/__init__.cpython-36.pyc toolfactory/galaxyxml/tool/import_xml.py toolfactory/galaxyxml/tool/parameters/__init__.py toolfactory/galaxyxml/tool/parameters/__pycache__/__init__.cpython-36.pyc |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/galaxyxml/__init__.py --- a/toolfactory/galaxyxml/__init__.py Wed Aug 12 01:43:46 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,64 +0,0 @@ -from builtins import object -from builtins import str - -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 |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/galaxyxml/__pycache__/__init__.cpython-36.pyc |
| b |
| Binary file toolfactory/galaxyxml/__pycache__/__init__.cpython-36.pyc has changed |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/galaxyxml/tool/__init__.py --- a/toolfactory/galaxyxml/tool/__init__.py Wed Aug 12 01:43:46 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,181 +0,0 @@ -import copy -import logging - -from galaxyxml import GalaxyXML, Util -from galaxyxml.tool.parameters import XMLParam - -from lxml import etree - -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: - 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() |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/galaxyxml/tool/__pycache__/__init__.cpython-36.pyc |
| b |
| Binary file toolfactory/galaxyxml/tool/__pycache__/__init__.cpython-36.pyc has changed |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/galaxyxml/tool/import_xml.py --- a/toolfactory/galaxyxml/tool/import_xml.py Wed Aug 12 01:43:46 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,713 +0,0 @@\n-import logging\n-import xml.etree.ElementTree as ET\n-\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(\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- 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> tag.\n- :type requirements_root: :class:`xml.etree._Element`\n- """'..b')\n- outputs_root.append(collection)\n-\n- def _load_discover_datasets(self, root, disc_root):\n- """\n- Add <discover_datasets> to root (<collection>).\n-\n- :param root: root to append <collection> to.\n- :param disc_root: root of <discover_datasets> tag.\n- :param disc_root: :class:`xml.etree._Element`\n- """\n- root.append(\n- gxtp.DiscoverDatasets(\n- 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- 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(\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- 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(\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- 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' |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/galaxyxml/tool/parameters/__init__.py --- a/toolfactory/galaxyxml/tool/parameters/__init__.py Wed Aug 12 01:43:46 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,739 +0,0 @@\n-from builtins import object\n-from builtins import str\n-\n-from galaxyxml import Util\n-\n-from lxml import etree\n-\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(\n- "Child was unacceptable to parent (%s is not appropriate for %s)" % (type(self), type(sub_node))\n- )\n- else:\n- raise Exception(\n- "Child was unacceptable to parent (%s is not appropriate for %s)" % (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- # 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, chil'..b'e"):\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 isinstance(child, ChangeFormat) or 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__(\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) 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, 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__(\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-\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' |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/galaxyxml/tool/parameters/__pycache__/__init__.cpython-36.pyc |
| b |
| Binary file toolfactory/galaxyxml/tool/parameters/__pycache__/__init__.cpython-36.pyc has changed |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Wed Aug 12 01:43:46 2020 -0400 +++ b/toolfactory/rgToolFactory2.py Wed Aug 12 19:00:44 2020 -0400 |
| b |
| @@ -17,8 +17,10 @@ # removed all the old complications including making the new tool use this same script # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml # No support for automatic HTML file creation from arbitrary outputs -# TODO: add option to run that code as a post execution hook -# TODO: add additional history input parameters - currently only one +# essential problem is to create two command lines - one for the tool xml and a different +# one to run the executable with the supplied test data and settings +# Be simpler to write the tool, then run it with planemo and soak up the test outputs. + import argparse @@ -249,6 +251,8 @@ ) art = "%s.%s" % (self.tool_name, self.args.interpreter_name) artifact = open(art, "wb") + if self.args.interpreter_name == "python": + artifact.write(bytes("#!/usr/bin/env python\n", "utf8")) artifact.write(bytes(self.script, "utf8")) artifact.close() aCL(self.args.interpreter_name) @@ -541,7 +545,8 @@ ) self.tool.add_comment("Source in git at: %s" % (toolFactoryURL)) self.tool.add_comment( - "Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573" + "Cite: Creating re-usable tools from scripts doi: \ + 10.1093/bioinformatics/bts573" ) exml = self.tool.export() xf = open('%s.xml' % self.tool_name, "w") |
| b |
| diff -r a30536c100bf -r 2cd6555baf44 toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Wed Aug 12 01:43:46 2020 -0400 +++ b/toolfactory/rgToolFactory2.xml Wed Aug 12 19:00:44 2020 -0400 |
| [ |
| @@ -122,7 +122,7 @@ </macros> <requirements> <requirement type="package">python</requirement> - <requirement type="package">lxml</requirement> + <requirement type="package">galaxyxml</requirement> </requirements> <command interpreter="python"><![CDATA[ #import os |