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Implement <filter> tag for output collections.

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Closes #445.
This commit is contained in:
John Chilton
2015-07-14 10:18:24 +01:00
parent ec36199a27
commit 163b0e37ca
4 changed files with 57 additions and 1 deletions
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lib/galaxy/tools/evaluation.py
+2 -1
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@@ -329,7 +329,8 @@ class ToolEvaluator( object ):
# Assume the reason we lack this output is because a filter
# failed to pass; for tool writing convienence, provide a
# NoneDataset
param_dict[ out_name ] = NoneDataset( datatypes_registry=self.app.datatypes_registry, ext=output.format )
ext = getattr( output, "format", None ) # populate only for output datasets (not collections)
param_dict[ out_name ] = NoneDataset( datatypes_registry=self.app.datatypes_registry, ext=ext )
def __populate_non_job_params(self, param_dict):
# -- Add useful attributes/functions for use in creating command line.
lib/galaxy/tools/parser/xml.py
+2
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@@ -186,6 +186,7 @@ class XmlToolSource(ToolSource):
inherit_metadata = string_as_bool( collection_elem.get( "inherit_metadata", None ) )
default_format_source = collection_elem.get( "format_source", None )
default_metadata_source = collection_elem.get( "metadata_source", "" )
filters = collection_elem.findall( 'filter' )
dataset_collectors = None
if collection_elem.find( "discover_datasets" ) is not None:
@@ -199,6 +200,7 @@ class XmlToolSource(ToolSource):
name,
structure,
label=label,
filters=filters,
default_format=default_format,
inherit_format=inherit_format,
inherit_metadata=inherit_metadata,
test/functional/tools/output_collection_filter.xml
+52
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@@ -0,0 +1,52 @@
<tool id="output_collection_filter" name="output_collection_filter" version="1.0.0">
<command>
echo "AF" > af.txt;
echo "AR" > ar.txt;
echo "BF" > bf.txt;
echo "BR" > br.txt;
</command>
<inputs>
<param name="output_type" type="select" label="Output Type">
<option value="a">A</option>
<option value="b">B</option>
</param>
</inputs>
<outputs>
<collection name="a_paired_output" type="paired" label="A Pair">
<data name="forward" format="txt" from_work_dir="af.txt" />
<data name="reverse" format="txt" from_work_dir="ar.txt" />
<filter>output_type == "a"</filter>
</collection>
<collection name="b_paired_output" type="paired" label="B Pair">
<data name="forward" format="txt" from_work_dir="bf.txt" />
<data name="reverse" format="txt" from_work_dir="br.txt" />
<filter>output_type == "b"</filter>
</collection>
</outputs>
<tests>
<!-- TODO: Enhance test cases to actually verify other collection not
created. -->
<test>
<param name="output_type" value="a" />
<output_collection name="a_paired_output" type="paired">
<element name="forward" ftype="txt">
<assert_contents><has_line line="AF" /></assert_contents>
</element>
<element name="reverse" ftype="txt">
<assert_contents><has_line line="AR" /></assert_contents>
</element>
</output_collection>
</test>
<test>
<param name="output_type" value="b" />
<output_collection name="b_paired_output" type="paired">
<element name="forward" ftype="txt">
<assert_contents><has_line line="BF" /></assert_contents>
</element>
<element name="reverse" ftype="txt">
<assert_contents><has_line line="BR" /></assert_contents>
</element>
</output_collection>
</test>
</tests>
</tool>
test/functional/tools/samples_tool_conf.xml
+1
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@@ -27,6 +27,7 @@
<tool file="output_order.xml" />
<tool file="output_format.xml" />
<tool file="output_filter.xml" />
<tool file="output_collection_filter.xml" />
<tool file="output_auto_format.xml" />
<tool file="disambiguate_repeats.xml" />
<tool file="min_repeat.xml" />