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[24.0] Create harmonized collections from correct tool outputs #19222

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merged 3 commits into from
Dec 2, 2024
Merged

[24.0] Create harmonized collections from correct tool outputs #19222

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a42d7f3
Create harmonized collections from correct tool outputs
wm75 Nov 29, 2024
129b8a2
Fix test file type
wm75 Nov 29, 2024
891d7aa
Try to fix tool test
wm75 Nov 29, 2024
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7 changes: 3 additions & 4 deletions lib/galaxy/tools/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3660,14 +3660,13 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
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

Expand All @@ -3685,7 +3684,7 @@ def output_with_selected_identifiers(old_elements_dict, output_label):
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:
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31 changes: 31 additions & 0 deletions lib/galaxy/tools/harmonize_two_collections_list.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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.fastqsanger" 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.fastqsanger" ftype="fastqsanger" />
<element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
</element>
</output_collection>
</test>
</tests>
<help><![CDATA[

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