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Updating tools/mzmine to 4.7.8 #7171

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Updating tools/mzmine to 4.7.8 #7171

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2437a2a
Updating tools/mzmine from version 3.9.0 to 4.7.8
Jul 21, 2025
37e9e08
Try updating mzmine to 4.7.8
SaimMomin12 Jul 24, 2025
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1 change: 0 additions & 1 deletion tools/mzmine/.lint_skip
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20 changes: 10 additions & 10 deletions tools/mzmine/mzmine_batch.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<tool id="mzmine_batch" name="MZMine batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
<tool id="mzmine_batch" name="MZMine batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
<macros>
<token name="@TOOL_VERSION@">3.9.0</token>
<token name="@TOOL_VERSION@">4.7.8</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<xrefs>
Expand Down Expand Up @@ -70,9 +70,9 @@
</collection>
</outputs>
<tests>
<!-- <test>
<test>
<param name="batch" value="test_small.xml" ftype="xml"/>
<param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
<param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine/refs/heads/master/mzmine-community/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine/refs/heads/master/mzmine-community/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
<param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
<output_collection name="output" count="3" type="list">
<element name="test2_iimn_gnps" ftype="mgf">
Expand All @@ -98,11 +98,11 @@
<has_text text="INFO: Starting processing of task Local CSV identification using database" negate="true"/>
<has_text text="INFO: Finished a batch of 11 steps"/>
</assert_stderr>
</test> -->
</test>
<!-- test with localdb -->
<!-- <test>
<test>
<param name="batch" value="test_localdatabase.xml" ftype="xml"/>
<param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
<param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine/refs/heads/master/mzmine-community/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine/refs/heads/master/mzmine-community/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
<param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
<param name="localdb" value="local_database.csv" ftype="csv"/>
<output_collection name="output" count="3" type="list">
Expand All @@ -129,16 +129,16 @@
<has_text text="INFO: Starting processing of task Local CSV identification using database"/>
<has_text text="INFO: Finished a batch of 12 steps"/>
</assert_stderr>
</test> -->
</test>
<!-- test with localdb in batch, but user does not provide one-->
<!-- <test expect_failure="true" expect_exit_code="1">
<test expect_failure="true" expect_exit_code="1">
<param name="batch" value="test_localdatabase.xml" ftype="xml"/>
<param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
<param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
<assert_stderr>
<has_text text="Batch file contains LocalCSVDatabaseSearchModule but no local DB CSV file given"/>
</assert_stderr>
</test> -->
</test>
</tests>
<help><![CDATA[
MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data.
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