add example and test for MacrosTool

- plus docs

- also return at least some TODO in the CLI
  generated for output collections

Author: bernt-matthias

.travis.yml

@@ -9,6 +9,8 @@ script:
 - flake8 galaxyxml --ignore=E2,E3,E4,E5,W3,W505,C901,E501
 - python examples/example.py > tmp.xml
 - xmldiff tmp.xml examples/tool.xml
+- python examples/example_macros.py > tmp.xml
+- xmldiff tmp.xml examples/example_macros.xml
 - nosetests --with-coverage --cover-package=galaxyxml
 deploy:
   provider: pypi

examples/example_macros.py

@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+import galaxyxml.tool as gxt
+import galaxyxml.tool.parameters as gxtp
+
+# examplify the use of MacrosTool
+# 
+
+tool = gxt.MacrosTool(
+    name="aragorn",
+    id="aragorn",
+    version="1.2.36",
+    description="Aragorn is a tRNA finder",
+    executable="aragorn.exe",
+    version_command="aragorn.exe --version",
+)
+
+inputs = tool.inputs
+outputs = tool.outputs
+
+# Add requirements
+requirements = gxtp.Requirements()
+requirements.append(gxtp.Requirement("package", "samtools", version="1.0.0"))
+requirements.append(gxtp.Container("docker", "one_super_image"))
+tool.requirements = requirements
+
+# 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 in a section
+section = gxtp.Section("float_section", "Float section")
+param = gxtp.FloatParam("float", label="Float label", help="Float help", value=0, num_dashes=1)
+param.space_between_arg = " "
+section.append(param)
+inputs.append(section)
+
+# A conditional
+param = gxtp.Conditional("cond", label="Conditional")
+param.append(gxtp.SelectParam("Select", options={"hi": "1", "bye": "2"}))
+when_a = gxtp.When(value="hi")
+when_b = gxtp.When(value="bye")
+when_b.append(gxtp.IntegerParam("some_int", value=0, num_dashes=1, label="Advanced value"))
+param.append(when_a)
+param.append(when_b)
+inputs.append(param)
+
+# Integer parameters
+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)
+
+posint = gxtp.IntegerParam("posint", label="posint label", positional=True, help="posinthelp", value=0, num_dashes=2)
+
+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)
+inputs.append(posint)
+
+# Add Select with options from_file with columns and filter
+param = gxtp.SelectParam("select_local")
+options = gxtp.Options(from_file="loc_file.loc")
+column_a = gxtp.Column("name", 0)
+options.append(column_a)
+column_b = gxtp.Column("value", 1)
+options.append(column_b)
+filter_a = gxtp.Filter("sort_by", name="sorted", column="1")
+options.append(filter_a)
+param.append(options)
+inputs.append(param)
+
+# Configfiles
+configfiles = gxtp.Configfiles()
+configfiles.append(gxtp.Configfile(name="testing", text="Hello <> World"))
+configfiles.append(gxtp.ConfigfileDefaultInputs(name="inputs"))
+
+# Outputs
+param = gxtp.OutputData("output", format="tabular", num_dashes=1)
+param.space_between_arg = " "
+outputs.append(param)
+# Collection
+collection = gxtp.OutputCollection("supercollection", label="a small label")
+discover = gxtp.DiscoverDatasets("(?P&lt;designation&gt;.+)\.pdf.fasta", format="fasta")
+collection.append(discover)
+outputs.append(collection)
+
+tool.inputs = inputs
+tool.outputs = outputs
+tool.help = "HI"
+tool.configfiles = configfiles
+
+# Add Tests sections
+tool.tests = gxtp.Tests()
+test_a = gxtp.Test()
+param = gxtp.TestParam("float", value=5.4)
+test_a.append(param)
+test_out = gxtp.TestOutput(name="output", value="file.out")
+test_a.append(test_out)
+tool.tests.append(test_a)
+
+
+# Add comment to the wrapper
+tool.add_comment("This tool descriptor has been generated using galaxyxml.")
+
+print(tool.export())

examples/example_macros.xml

@@ -212,7 +212,22 @@ def export(self, keep_old_command=False):
 
 
 class MacrosTool(Tool):
+    """
+    creates a <macros> tag containing macros and tokens
+    for the inputs and outputs:
 
+    for the inputs 
+
+    - a macro `<xml name="ID_inmacro">` containing all the inputs
+    - a token `<token name="ID_INMACRO">` containing the CLI for the inputs
+
+    where ID is the id used in initialization.
+
+    analogously for the outputs `ID_outmacro` and `ID_OUTMACRO`
+    are created.
+
+    TODO all other elements, like requirements are currently ignored
+    """
     def __init__(self, *args, **kwargs):
         super(MacrosTool, self).__init__(*args, **kwargs)
         self.root = etree.Element('macros')
@@ -235,6 +250,7 @@ def export(self, keep_old_command=False):  # noqa
             command_line.append(export_xml.inputs.cli())
         except Exception as e:
             logger.warning(str(e))
+            raise
 
         # Add command section
         command_node = etree.SubElement(export_xml.root, 'token', {"name": "%s_INMACRO" % self.id.upper()})

galaxyxml/tool/__init__.py

@@ -77,8 +77,7 @@ class Macros(XMLParam):
     name = "macros"
 
     def acceptable_child(self, child):
-        return isinstance(child, Macro) \
-               or isinstance(child, Import)
+        return isinstance(child, (Macro, Import))
 
 
 class Macro(XMLParam):
@@ -91,8 +90,7 @@ def __init__(self, name):
         super(Macro, self).__init__(**passed_kwargs)
 
     def acceptable_child(self, child):
-        return issubclass(type(child), XMLParam) \
-               and not isinstance(child, Macro)
+        return issubclass(type(child), XMLParam) and not isinstance(child, Macro)
 
 
 class Import(XMLParam):
@@ -103,8 +101,7 @@ def __init__(self, value):
         self.node.text = value
 
     def acceptable_child(self, child):
-        return issubclass(type(child), XMLParam) \
-               and not isinstance(child, Macro)
+        return issubclass(type(child), XMLParam) and not isinstance(child, Macro)
 
 
 class Expand(XMLParam):
@@ -789,6 +786,8 @@ def __init__(
     def acceptable_child(self, child):
         return isinstance(child, OutputData) or isinstance(child, OutputFilter) or isinstance(child, DiscoverDatasets)
 
+    def command_line(self):
+        return "## TODO CLI for OutputCollection %s" % self.name
 
 class DiscoverDatasets(XMLParam):
     name = "discover_datasets"