[med-svn] [python-galaxyxml] 07/11: Change repo structure
Andreas Tille
tille at debian.org
Sat Jan 14 14:55:23 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-galaxyxml.
commit 78588606c0fa7eceb1d8c16d9b6dc5680e5fe1d5
Author: Anton Khodak <anton.khodak at ukr.net>
Date: Sat Jan 14 16:10:30 2017 +0200
Change repo structure
---
0.1.tar.gz | Bin 7225 -> 0 bytes
README.md | 20 --
examples/example.py | 51 -----
examples/tool.xml | 20 --
galaxyxml/__init__.py | 47 ----
galaxyxml/tool/__init__.py | 103 ---------
galaxyxml/tool/parameters/__init__.py | 400 ----------------------------------
parser.py | 119 ----------
python-galaxyxml_0.1.orig.tar.gz | 1 -
requirements.txt | 1 -
setup.py | 19 --
11 files changed, 781 deletions(-)
diff --git a/0.1.tar.gz b/0.1.tar.gz
deleted file mode 100644
index 9e4d8f5..0000000
Binary files a/0.1.tar.gz and /dev/null differ
diff --git a/README.md b/README.md
deleted file mode 100644
index 32dcbe7..0000000
--- a/README.md
+++ /dev/null
@@ -1,20 +0,0 @@
-# Galaxy XML Generation Libraries
-
-These libraries will support building of Tool XML and Tool Dependencies XML.
-We'd be happy to support any other XML that Galaxy supports, just make an issue
-or PR if you're feeling motivated.
-
-## Status
-
-- ToolXML is mostly supported, there
-
-## Known Bugs
-
-- no validation of unique names
-- repeats aren't named properly
-- conditional/whens aren't named properly
-- conditionals not handled in CLI
-
-## License
-
-- Apache License, v2
diff --git a/examples/example.py b/examples/example.py
deleted file mode 100644
index c97d48a..0000000
--- a/examples/example.py
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/usr/bin/env python
-import galaxyxml.tool as gxt
-import galaxyxml.tool.parameters as gxtp
-
-tool = gxt.Tool("aragorn", 'se.lu.mbioekol.mbio-serv2.aragorn',
- "1.2.36", "Aragorn is a tRNA finder", "aragorn.exe")
-
-inputs = gxtp.Inputs()
-outputs = gxtp.Outputs()
-
-# A parameter
-param = gxtp.BooleanParam('flag', label='Flag label', help='Flag help', num_dashes=1)
-# Yes I know this is rubbish. Please make a PR!!
-param.space_between_arg = ' '
-inputs.append(param)
-
-
-# A float
-param = gxtp.FloatParam('float', label='Float label',
- help='Float help', value=0, num_dashes=1)
-param.space_between_arg = ' '
-inputs.append(param)
-
-
-param_min = gxtp.IntegerParam('int_min',
- label='int_min label',
- help='int_min help', value=0, num_dashes=1)
-param_max = gxtp.IntegerParam('int_max',
- label='int_max label',
- help='int_max help', value=0, num_dashes=1)
-param_min.command_line_override = '-i$int_min,$int_max'
-param_max.command_line_override = ''
-param_min.space_between_arg = ' '
-param_max.space_between_arg = ' '
-inputs.append(param_min)
-inputs.append(param_max)
-
-
-# Outputs
-param = gxtp.OutputParameter('output', format="tabular", num_dashes=1)
-param.space_between_arg = ' '
-outputs.append(param)
-
-tool.inputs = inputs
-tool.outputs = outputs
-tool.help = 'HI'
-
-data = tool.export()
-
-with open('tool.xml', 'w') as handle:
- handle.write(data)
diff --git a/examples/tool.xml b/examples/tool.xml
deleted file mode 100644
index a7c64a8..0000000
--- a/examples/tool.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<tool force_history_refresh="false" hidden="false" id="se.lu.mbioekol.mbio-serv2.aragorn" name="aragorn" version="1.2.36" workflow_compatible="true">
- <description>Aragorn is a tRNA finder</description>
- <stdio>
- <exit_code level="fatal" range="1:"/>
- </stdio>
- <command><![CDATA[aragorn.exe $flag
--float $float
--i$int_min,$int_max
--output $output]]></command>
- <inputs>
- <param checked="false" help="(-flag) Flag help" label="Flag label" name="flag" type="boolean" truevalue="-flag"/>
- <param help="(-float) Float help" label="Float label" name="float" type="float" value="0"/>
- <param help="(-int_min) int_min help" label="int_min label" name="int_min" type="integer" value="0"/>
- <param help="(-int_max) int_max help" label="int_max label" name="int_max" type="integer" value="0"/>
- </inputs>
- <outputs>
- <data format="tabular" hidden="false" name="output"/>
- </outputs>
- <help><![CDATA[HI]]></help>
-</tool>
diff --git a/galaxyxml/__init__.py b/galaxyxml/__init__.py
deleted file mode 100644
index 0d2e959..0000000
--- a/galaxyxml/__init__.py
+++ /dev/null
@@ -1,47 +0,0 @@
-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)
-
-
-class Util(object):
-
- @classmethod
- def coerce(cls, data):
- """Recursive data sanitisation
- """
- if isinstance(data, dict):
- return {k: cls.coerce(v) for k, v in data.items() if v is not None}
- elif isinstance(data, list):
- return [cls.coerce(v) 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):
- if 'kwargs' in params:
- kwargs = params['kwargs']
- for k in kwargs:
- params[k] = kwargs[k]
- del params['kwargs']
- del params['self']
- return params
diff --git a/galaxyxml/tool/__init__.py b/galaxyxml/tool/__init__.py
deleted file mode 100644
index 6e077df..0000000
--- a/galaxyxml/tool/__init__.py
+++ /dev/null
@@ -1,103 +0,0 @@
-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')
-
-
-class Tool(GalaxyXML):
-
- def __init__(self, name, id, version, description, executable, hidden=False,
- tool_type=None, URL_method=None, workflow_compatible=True,
- force_history_refresh=False, interpreter=None):
-
- self.executable = executable
- self.interpreter = interpreter
- kwargs = {
- 'name': name,
- 'id': id,
- 'version': version,
- 'hidden': hidden,
- 'workflow_compatible': workflow_compatible,
- 'force_history_refresh': force_history_refresh,
- }
- 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 version_command(self, command_string):
- version_command = etree.SubElement(self.root, 'version_command')
- version_command.text = version_command
-
- 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):
- command_line = []
- try:
- command_line.append(self.inputs.cli())
- except Exception, e:
- print e
-
- try:
- command_line.append(self.outputs.cli())
- except:
- pass
-
- # Add stdio section
- stdio = etree.SubElement(self.root, 'stdio')
- etree.SubElement(stdio, 'exit_code', range='1:', level='fatal')
-
- # Steal interpreter from kwargs
- command_kwargs = {}
- if self.interpreter is not None:
- command_kwargs['interpreter'] = self.interpreter
-
- # Add command section
- command_node = etree.SubElement(self.root, 'command', **command_kwargs)
-
- actual_cli = "%s %s" % (self.executable, self.clean_command_string(command_line))
- command_node.text = etree.CDATA(actual_cli.strip())
-
-
- try:
- self.append(self.inputs)
- except:
- pass
-
- try:
- self.append(self.outputs)
- except:
- pass
-
- help_element = etree.SubElement(self.root, 'help')
- help_element.text = etree.CDATA(self.help)
-
- return super(Tool, self).export()
diff --git a/galaxyxml/tool/parameters/__init__.py b/galaxyxml/tool/parameters/__init__.py
deleted file mode 100644
index 1703adb..0000000
--- a/galaxyxml/tool/parameters/__init__.py
+++ /dev/null
@@ -1,400 +0,0 @@
-from lxml import etree
-from galaxyxml import Util
-
-class XMLParam(object):
- name = 'node'
-
- def __init__(self, *args, **kwargs):
- # http://stackoverflow.com/a/12118700
- self.children = []
- kwargs = {k: v for k, v in kwargs.items() if v is not None}
- kwargs = Util.coerce(kwargs)
- self.node = etree.Element(self.name, **kwargs)
-
- def append(self, sub_node):
- if self.acceptable_child(sub_node):
- # If one of ours, they aren't etree nodes, they're custom objects
- if issubclass(type(sub_node), XMLParam):
- self.node.append(sub_node.node)
- self.children.append(sub_node)
- else:
- raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % (type(self), type(sub_node)))
- else:
- raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % (type(self), type(sub_node)))
-
- def validate(self):
- # Very few need validation, but some nodes we may want to have
- # validation routines on. Should only be called when DONE.
- for child in self.children:
- # If any child fails to validate return false.
- if not child.validate():
- return False
- return True
-
- def cli(self):
- lines = []
- for child in self.children:
- lines.append(child.command_line())
- #lines += child.command_line()
- return '\n'.join(lines)
-
- def command_line(self):
- return None
-
-
-class RequestParamTranslation(XMLParam):
- name = 'request_param_translation'
-
- def __init__(self, **kwargs):
- self.node = etree.Element(self.name)
-
- def acceptable_child(self, child):
- return isinstance(child, RequestParamTranslation)
-
-
-class RequestParam(XMLParam):
- name = 'request_param'
-
- def __init__(self, galaxy_name, remote_name, missing, **kwargs):
- #TODO: bulk copy locals into self.attr?
- self.galaxy_name = galaxy_name
- # http://stackoverflow.com/a/1408860
- params = Util.clean_kwargs(locals().copy())
- super(RequestParam, self).__init__(**params)
-
- def acceptable_child(self, child):
- return isinstance(child, AppendParam) and self.galaxy_name == "URL"
-
-
-class AppendParam(XMLParam):
- name = 'append_param'
-
- def __init__(self, separator="&", first_separator="?", join="=", **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(AppendParam, self).__init__(**params)
-
- def acceptable_child(self, child):
- return isinstance(child, AppendParamValue)
-
-
-class AppendParamValue(XMLParam):
- name = 'value'
-
- def __init__(self, name="_export", missing="1", **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(AppendParamValue, self).__init__(**params)
-
- def acceptable_child(self, child):
- return False
-
-
-class Inputs(XMLParam):
- name = 'inputs'
- # This bodes to be an issue -__-
-
- def acceptable_child(self, child):
- return issubclass(type(child), InputParameter)
-
-
-class InputParameter(XMLParam):
-
- def __init__(self, name, **kwargs):
- # TODO: look at
- self.mako_identifier = name
- # We use kwargs instead of the usual locals(), so manually copy the
- # name to kwargs
- kwargs['name'] = name
-
- # Handle positional parameters
- if 'positional' in kwargs and kwargs['positional']:
- self.positional = True
- else:
- self.positional = False
-
- if 'num_dashes' in kwargs:
- self.num_dashes = kwargs['num_dashes']
- del kwargs['num_dashes']
- else:
- self.num_dashes = 0
-
- self.space_between_arg = " "
-
- # Not sure about this :(
- # https://wiki.galaxyproject.org/Tools/BestPractices#Parameter_help
- if 'label' in kwargs:
- # TODO: replace with positional attribute
- if len(self.flag()) > 0:
- if kwargs['label'] is None:
- kwargs['label'] = 'Author did not provide help for this parameter... '
- if not self.positional:
- kwargs['label'] += ' (%s)' % self.flag()
-
- super(InputParameter, self).__init__(**kwargs)
-
- def command_line(self):
- before = self.command_line_before()
- cli = self.command_line_actual()
- after = self.command_line_after()
-
- complete = [x for x in (before, cli, after) if x is not None]
- return '\n'.join(complete)
-
- def command_line_before(self):
- return None
-
- def command_line_after(self):
- return None
-
- def command_line_actual(self):
- if hasattr(self, 'command_line_override'):
- return self.command_line_override
- else:
- if self.positional:
- return self.mako_name()
- else:
- return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name())
-
- def mako_name(self):
- # TODO: enhance logic to check up parents for things like repeat>condotion>param
- return '$' + self.mako_identifier
-
- def flag(self):
- flag = '-' * self.num_dashes
- return flag + self.mako_identifier
-
-
-class Repeat(InputParameter):
- name = 'repeat'
-
- def __init__(self, name, title, min=None, max=None, default=None,
- **kwargs):
- params = Util.clean_kwargs(locals().copy())
- # Allow overriding
- self.cli_before = '#for $i in $%s' % name
- self.cli_after = '#end for'
- super(Repeat, self).__init__(**params)
-
- def acceptable_child(self, child):
- return issubclass(type(child), InputParameter)
-
- def command_line_before(self):
- return self.cli_before
-
- def command_line_after(self):
- return self.cli_after
-
- def command_line_actual(self):
- if hasattr(self, 'command_line_override'):
- return self.command_line_override
- else:
- return "%s" % self.mako_name()
-
-class Conditional(InputParameter):
- name = 'conditional'
-
- def __init__(self, name, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(Conditional, self).__init__(**params)
-
- def acceptable_child(self, child):
- return issubclass(type(child), InputParameter) \
- and not isinstance(child, Conditional)
-
- def validate(self):
- # Find a way to check if one of the kids is a WHEN
- pass
-
-
-class Param(InputParameter):
- name = 'param'
-
- # This...isn't really valid as-is, and shouldn't be used.
- def __init__(self, name, optional=None, label=None, help=None, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- params['type'] = self.type
- super(Param, self).__init__(**params)
-
- if type(self) == Param:
- raise Exception("Param class is not an actual parameter type, use a subclass of Param")
-
- def acceptable_child(self, child):
- return issubclass(type(child, InputParameter) or isinstance(child), ValidatorParam)
-
-
-class TextParam(Param):
- type = 'text'
-
- def __init__(self, name, optional=None, label=None, help=None, size=None,
- area=False, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(TextParam, self).__init__(**params)
-
-
-class _NumericParam(Param):
-
- def __init__(self, name, value, optional=None, label=None, help=None,
- min=None, max=None, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(_NumericParam, self).__init__(**params)
-
-
-class IntegerParam(_NumericParam):
- type = 'integer'
-
-
-class FloatParam(_NumericParam):
- type = 'float'
-
-
-class BooleanParam(Param):
- type = 'boolean'
-
- def __init__(self, name, optional=None, label=None, help=None,
- checked=False, truevalue=None, falsevalue=None, **kwargs):
- params = Util.clean_kwargs(locals().copy())
-
- super(BooleanParam, self).__init__(**params)
- if truevalue is None and falsevalue is None:
- # If truevalue and falsevalue are None, then we use "auto", the IUC
- # recommended default.
- #
- # truevalue is set to the parameter's value, and falsevalue is not.
- #
- # Unfortunately, mako_identifier is set as a result of the super
- # call, which we shouldn't call TWICE, so we'll just hack around this :(
- #params['truevalue'] = '%s%s' % (self.)
- self.node.attrib['truevalue'] = self.flag()
-
-
- def command_line_actual(self):
- if hasattr(self, 'command_line_override'):
- return self.command_line_override
- else:
- return "%s" % self.mako_name()
-
-
-class DataParam(Param):
- type = 'data'
-
- def __init__(self, name, optional=None, label=None, help=None, format=None,
- multiple=None, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(DataParam, self).__init__(**params)
-
-
-class SelectParam(Param):
- type = 'data'
-
- def __init__(self, name, optional=None, label=None, help=None,
- data_ref=None, display=None, multiple=None, options=None,
- default=None, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- del params['options']
- del params['default']
-
- super(DataParam, self).__init__(**params)
-
- if options is not None and default is not None:
- if default not in options:
- raise Exception("Specified a default that isn't in options")
-
- for k,v in options:
- selected = (k == default)
- self.append(SelectOption(k, v, selected=selected))
-
-
-class SelectOption(InputParameter):
- name = 'option'
-
- def __init__(self, value, text, selected=False, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- del params['text']
- super(SelectOption, self).__init__(**params)
- self.node.text = text
-
-
-class ValidatorParam(InputParameter):
- name = 'validator'
-
- def __init__(self, type, message=None, filename=None, metadata_name=None,
- metadata_column=None, line_startswith=None, min=None,
- max=None, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(ValidatorParam, self).__init__(**params)
-
-
-class Outputs(XMLParam):
- name = 'outputs'
-
- def acceptable_child(self, child):
- return issubclass(type(child), OutputParameter)
-
-
-class OutputParameter(XMLParam):
- """Copypasta of InputParameter, needs work
- """
- name = 'data'
-
- def __init__(self, name, format, format_source=None, metadata_source=None,
- label=None, from_work_dir=None, hidden=False, **kwargs):
- # TODO: validate format_source&metadata_source against something in the
- # XMLParam children tree.
- self.mako_identifier = name
- if 'num_dashes' in kwargs:
- self.num_dashes = kwargs['num_dashes']
- del kwargs['num_dashes']
- else:
- self.num_dashes = 0
- self.space_between_arg = " "
- params = Util.clean_kwargs(locals().copy())
-
- super(OutputParameter, self).__init__(**params)
-
- def command_line(self):
- if hasattr(self, 'command_line_override'):
- return self.command_line_override
- else:
- return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name())
-
- def mako_name(self):
- return '$' + self.mako_identifier
-
- def flag(self):
- flag = '-' * self.num_dashes
- return flag + self.mako_identifier
-
- def acceptable_child(self, child):
- return isinstance(child, OutputFilter) or isinstance(child, ChangeFormat)
-
-class OutputFilter(XMLParam):
- name = 'filter'
-
- def __init__(self, text, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- del params['text']
- super(OutputFilter, self).__init__(**params)
- self.node.text = text
-
- def acceptable_child(self, child):
- return False
-
-class ChangeFormat(XMLParam):
- name = 'change_format'
-
- def __init__(self, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(ChangeFormat, self).__init__(**params)
-
- def acceptable_child(self, child):
- return isinstance(child, ChangeFormatWhen)
-
-
-class ChangeFormatWhen(XMLParam):
- name = 'when'
-
- def __init__(self, input, format, value, **kwargs):
- params = Util.clean_kwargs(locals().copy())
- super(ChangeFormatWhen, self).__init__(**params)
-
- def acceptable_child(self, child):
- return False
diff --git a/parser.py b/parser.py
deleted file mode 100644
index e822ef6..0000000
--- a/parser.py
+++ /dev/null
@@ -1,119 +0,0 @@
-import re
-
-def start_pattern(string):
- return string.startswith(' -')
-
-
-CLI = {
- 'OUTPUT': (re.compile(r'^\s*(?P<dash>--?)(?P<name>[A-Za-z0-9]+)(?P<space_between_arg>[ ]*)<(?P<args>out[^>]*)>\s+(?P<content>.*)'), {'nargs': 1}),
- 'FLAG': (re.compile(r'^\s*(?P<dash>--?)(?P<name>[A-Za-z0-9]+)[ ]{2,}(?P<content>.*)'), {'nargs': 0}),
- 'PARAM': (re.compile(r'^\s*(?P<dash>--?)(?P<name>[A-Za-z0-9]+)(?P<space_between_arg>[ ]*)<(?P<args>[^>]*)>\s+(?P<content>.*)'), {'nargs': 1}),
- 'PARAM_RANGE': (re.compile(r'^\s*(?P<dash>--?)(?P<name>[A-Za-z0-9]+)(?P<space_between_arg>[ ]*)<(?P<args>[^>]*)>,<(?P<args2>[^>]*)>\s+(?P<content>.*)'), {'nargs': 2}),
-}
-
-CLI_GROUPS = ('name', 'args', 'content', 'args2', 'dash', 'space_between_arg')
-CLI_DEFAULTS = {
- 'space_between_arg': ' '
-}
-
-def detect_args(cli):
- for matcher in CLI:
- matches = CLI[matcher][0].search(cli)
- if matches:
- hit = CLI[matcher][1]
- hit['type'] = matcher
-
- # Apply defaults. Poorly organised.
- for default in CLI_DEFAULTS:
- hit[default] = CLI_DEFAULTS[default]
-
- # Actual groups in regex
- for group in CLI_GROUPS:
- try:
- hit[group] = matches.group(group)
- except IndexError:
- # Ignore missing groups
- pass
- return hit
- return None
-
-def reflow_block(block):
- single = ' '.join([x.strip() for x in block])
- return detect_args(single)
-
-def blocks(iterable):
- accumulator = []
- for line in iterable:
- if start_pattern(line):
- if accumulator:
- yield reflow_block(accumulator)
- accumulator = [line]
- else:
- accumulator.append(line)
- if accumulator:
- yield reflow_block(accumulator)
-
-import galaxyxml.tool as gxt
-import galaxyxml.tool.parameters as gxtp
-
-tool = gxt.Tool(name="aragorn", version="1.2.36", description="tRNA finder",
- executable="aragorn")
-inputs = gxtp.Inputs()
-outputs = gxtp.Outputs()
-for line in blocks(open('tmp','r').readlines()):
- if line and line['type'] == 'FLAG':
- param = gxtp.BooleanParam(line['name'], label=line['name'], help=line['content'],
- #truevalue=cli_param, falsevalue="")
- )
- param.num_dashes = len(line['dash'])
- param.space_between_arg = line['space_between_arg']
- inputs.append(param)
- elif line and line['type'] == 'PARAM':
- print "%(dash)s%(name)s <%(args)s> %(content)s" % line
- answer = raw_input("Is this a FLOAT, INT, or TEXT input? ")
- if 'FLOAT' in answer:
- param = gxtp.FloatParam(line['name'], label=line['name'],
- help=line['content'], value=0)
- elif 'INT' in answer:
- param = gxtp.IntegerParam(line['name'], label=line['name'],
- help=line['content'], value=0)
- elif 'TEXT' in answer:
- param = gxtp.TextParam(line['name'], label=line['name'],
- help=line['content'])
- try:
- param.num_dashes = len(line['dash'])
- param.space_between_arg = line['space_between_arg']
- inputs.append(param)
- except:
- print "Uhoh, bad answer"
- print
- elif line and line['type'] == 'PARAM_RANGE':
- param_min = gxtp.IntegerParam(line['name']+'_min',
- label=line['name']+'_min',
- help=line['content'], value=0)
- param_max = gxtp.IntegerParam(line['name']+'_max',
- label=line['name']+'_max',
- help=line['content'], value=0)
- param_min.command_line_override = '-i$i_min,$i_max'
- param_max.command_line_override = ''
- param_min.num_dashes = len(line['dash'])
- param_max.num_dashes = len(line['dash'])
- param_min.space_between_arg = line['space_between_arg']
- param_max.space_between_arg = line['space_between_arg']
- inputs.append(param_min)
- inputs.append(param_max)
- elif line and line['type'] == 'OUTPUT':
- param = gxtp.OutputParameter(line['name'], format="tabular")
- param.num_dashes = len(line['dash'])
- param.space_between_arg = line['space_between_arg']
- outputs.append(param)
-
-tool.inputs = inputs
-tool.outputs = outputs
-tool.help = 'HI'
-
-
-data = tool.export()
-
-with open('tool.xml', 'w') as handle:
- handle.write(data)
diff --git a/python-galaxyxml_0.1.orig.tar.gz b/python-galaxyxml_0.1.orig.tar.gz
deleted file mode 120000
index 1fafd7d..0000000
--- a/python-galaxyxml_0.1.orig.tar.gz
+++ /dev/null
@@ -1 +0,0 @@
-0.1.tar.gz
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index ab90481..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-lxml
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 90a9146..0000000
--- a/setup.py
+++ /dev/null
@@ -1,19 +0,0 @@
-from setuptools import setup
-
-requirements = [x.strip() for x in open('requirements.txt', 'r').readlines()]
-
-setup(name="galaxyxml",
- version='0.1',
- description='Galaxy XML generation library',
- author='Eric Rasche',
- author_email='rasche.eric at yandex.ru',
- license='GPL3',
- install_requires=requirements,
- packages=["galaxyxml", "galaxyxml.tool", "galaxyxml.tool.parameters"],
- classifiers=[
- 'Development Status :: 3 - Alpha',
- 'Operating System :: OS Independent',
- 'Intended Audience :: Developers',
- 'Environment :: Console',
- ],
- )
--
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