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Create harmonized collections from correct tool outputs

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This commit is contained in:
Wolfgang Maier
2024-11-29 16:59:11 +01:00
parent f4ab432ad6
commit a42d7f30a7
2 changed files with 34 additions and 4 deletions
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lib/galaxy/tools/__init__.py
+3 -4
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@@ -3660,14 +3660,13 @@ class HarmonizeTool(DatabaseOperationTool):
final_sorted_identifiers = [
element.element_identifier for element in elements1 if element.element_identifier in old_elements2_dict
]
# Raise Exception if it is empty
if len(final_sorted_identifiers) == 0:
# Create empty collections:
output_collections.create_collection(
next(iter(self.outputs.values())), "output1", elements={}, propagate_hda_tags=False
self.outputs["output1"], "output1", elements={}, propagate_hda_tags=False
)
output_collections.create_collection(
next(iter(self.outputs.values())), "output2", elements={}, propagate_hda_tags=False
self.outputs["output2"], "output2", elements={}, propagate_hda_tags=False
)
return
@@ -3685,7 +3684,7 @@ class HarmonizeTool(DatabaseOperationTool):
self._add_datasets_to_history(history, new_elements.values())
# Create collections:
output_collections.create_collection(
next(iter(self.outputs.values())), output_label, elements=new_elements, propagate_hda_tags=False
self.outputs[output_label], output_label, elements=new_elements, propagate_hda_tags=False
)
# Create outputs:
lib/galaxy/tools/harmonize_two_collections_list.xml
+31
View File
@@ -171,6 +171,37 @@
<output_collection name="output1" type="list" count="0"/>
<output_collection name="output2" type="list" count="0"/>
</test>
<!-- test that collection types get propagated to outputs correctly -->
<test>
<param name="input1">
<collection type="list">
<element name="element_1" value="simple_line.txt" />
</collection>
</param>
<param name="input2">
<collection type="list:paired">
<element name="element_1">
<collection type="paired">
<element name="forward" value="1.fastq" ftype="fastqsanger" />
<element name="reverse" value="1.fastqsanger" ftype="fastqsanger" />
</collection>
</element>
</collection>
</param>
<output_collection name="output1" type="list" count="1">
<element name="element_1">
<assert_contents>
<has_text_matching expression="^This is a line of text.\n$" />
</assert_contents>
</element>
</output_collection>
<output_collection name="output2" type="list:paired" count="1">
<element name="element_1">
<element name="forward" file="1.fastq" ftype="fastqsanger" />
<element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
</element>
</output_collection>
</test>
</tests>
<help><![CDATA[