diff --git a/examples/example.py b/examples/example.py index 0743758..00f3a65 100644 --- a/examples/example.py +++ b/examples/example.py @@ -88,7 +88,7 @@ outputs.append(param) # Collection collection = gxtp.OutputCollection("supercollection", label="a small label") -discover = gxtp.DiscoverDatasets("(?P<designation>.+)\.pdf.fasta", format="fasta") +discover = gxtp.DiscoverDatasets("(?P<designation>.+).pdf.fasta", format="fasta") collection.append(discover) outputs.append(collection) @@ -111,7 +111,7 @@ rep_out.append(param) test_a.append(rep_out) test_coll = gxtp.TestOutputCollection(name="pdf_out") -test_elem = gxtp.TestOCElement(name="apdf",file="apdf",ftype="pdf") +test_elem = gxtp.TestOCElement(name="apdf", file="apdf", ftype="pdf") test_coll.append(test_elem) test_a.append(test_coll) rep_out = gxtp.TestRepeat(name="output_repeat") diff --git a/examples/example_macros.py b/examples/example_macros.py index d8958b8..dc7924d 100644 --- a/examples/example_macros.py +++ b/examples/example_macros.py @@ -3,7 +3,7 @@ import galaxyxml.tool.parameters as gxtp # examplify the use of MacrosTool -# +# tool = gxt.MacrosTool( name="aragorn", @@ -57,6 +57,7 @@ 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) @@ -84,7 +85,7 @@ outputs.append(param) # Collection collection = gxtp.OutputCollection("supercollection", label="a small label") -discover = gxtp.DiscoverDatasets("(?P<designation>.+)\.pdf.fasta", format="fasta") +discover = gxtp.DiscoverDatasets("(?P<designation>.+).pdf.fasta", format="fasta") collection.append(discover) outputs.append(collection) diff --git a/test/unit_test_import_xml.py b/test/unit_test_import_xml.py index 0c7d18d..7560006 100644 --- a/test/unit_test_import_xml.py +++ b/test/unit_test_import_xml.py @@ -19,6 +19,7 @@ def test_stdio(self): self.assertEqual(std.attrib["level"], "fatal") self.assertEqual(std.attrib["range"], "1:") + class TestOverrides(TestImport): def test_override(self): co = "bash foo.sh > output1" @@ -199,20 +200,20 @@ def test_collection_output(self): def test_repeat(self): repeat = self.tool.tests.children[0].node[3] - self.assertEqual(repeat.attrib["name"],"testrepeat") + self.assertEqual(repeat.attrib["name"], "testrepeat") # test param within repeat self.assertEqual(repeat[0].attrib["name"], "repeatchild") self.assertEqual(repeat[0].attrib["value"], "foo") # test output within repeat output = self.tool.tests.children[0].node[4] - self.assertEqual(output.attrib["name"],"output_repeat") + self.assertEqual(output.attrib["name"], "output_repeat") self.assertEqual(output[0].attrib["file"], "outputchild") self.assertEqual(output[0].attrib["name"], "bar") def test_ocr(self): # test outputcollection within repeat - who knows... output = self.tool.tests.children[0].node[5] - self.assertEqual(output.attrib["name"],"collection_repeat") + self.assertEqual(output.attrib["name"], "collection_repeat") collection = output[0] self.assertEqual(collection.attrib["name"], "collectionchild") element = collection[0]