Commit a42d7f30 authored by Wolfgang Maier's avatar Wolfgang Maier
Browse files

Create harmonized collections from correct tool outputs

parent f4ab432a

lib/galaxy/tools/__init__.py

+3 −4
Original line number Diff line number Diff line
@@ -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 −0
Original line number Diff line number Diff line
@@ -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[