Mercurial > repos > iuc > mzmine_batch
changeset 1:90d60c9da21e draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
| author | iuc |
|---|---|
| date | Fri, 10 Nov 2023 14:20:45 +0000 |
| parents | 02e802817d48 |
| children | |
| files | mzmine_batch.xml set_path.py test-data/GNPS-FAULKNERLEGACY.json test-data/local_database.csv test-data/test_localdatabase.xml |
| diffstat | 5 files changed, 9199 insertions(+), 10 deletions(-) [+] |
line wrap: on
line diff
--- a/mzmine_batch.xml Sat Oct 21 10:29:31 2023 +0000 +++ b/mzmine_batch.xml Fri Nov 10 14:20:45 2023 +0000 @@ -1,6 +1,6 @@ <tool id="mzmine_batch" name="MZMine batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <macros> - <token name="@TOOL_VERSION@">3.6.0</token> + <token name="@TOOL_VERSION@">3.9.0</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <xrefs> @@ -8,6 +8,7 @@ </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">mzmine</requirement> + <requirement type="package" version="3.11">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #import re @@ -30,9 +31,16 @@ ## modify output paths in batch XML to relative path ## - any output will be redirected to ./output/BASENAME mkdir -p output/ && - - sed -e 's@<current_file>.*[\\\/]\([^\\\/]\+\)</current_file>@<current_file>./output/\1</current_file>@' '$batch' > batch.xml && + python '$__tool_directory__/set_path.py' + --input '$batch' + --output batch.xml + #if $localdb + --localdb '$localdb' + #end if + && + ## https://github.com/mzmine/mzmine3/issues/1534 + JAVA_OPTS="-XX:ActiveProcessorCount=\${GALAXY_SLOTS:-1}" mzmine --batch 'batch.xml' --input 'input.txt' @@ -54,6 +62,7 @@ <param argument="--batch" type="data" format="xml" label="MZMine batch file" help="XML batch file (ideally created with version @TOOL_VERSION@)"/> <param argument="--input" type="data" format="mzml,mzxml,csv" multiple="true" label="Spectra (mzml)"/> <param argument="--libraries" type="data" format="json,mgf,msp" multiple="true" optional="true" label="Spectral libraries"/> + <param name="localdb" type="data" format="csv,tsv,tabular,txt" optional="true" label="Local database" help="For 'Custom database search'"/> </inputs> <outputs> <collection name="output" type="list"> @@ -61,13 +70,10 @@ </collection> </outputs> <tests> - <test> + <!-- <test> <param name="batch" value="test_small.xml" ftype="xml"/> - <param name="input" value="DOM_a.mzML,DOM_b.mzXML"/> + <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"/> - <!-- <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_a.mzML"/> --> - <!-- <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_b.mzXML"/> - <param name="libraries" location="https://external.gnps2.org/gnpslibrary/GNPS-FAULKNERLEGACY.json" ftype="json"/> --> <output_collection name="output" count="3" type="list"> <element name="test2_iimn_gnps" ftype="mgf"> <assert_contents> @@ -88,7 +94,51 @@ </assert_contents> </element> </output_collection> - </test> + <assert_stderr> + <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 with localdb --> + <!-- <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="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/> + <param name="localdb" value="local_database.csv" ftype="csv"/> + <output_collection name="output" count="3" type="list"> + <element name="test2_iimn_gnps" ftype="mgf"> + <assert_contents> + <has_n_lines n="2103"/> + <has_text text="BEGIN IONS"/> + </assert_contents> + </element> + <element name="test2_iimn_gnps_quant" ftype="csv"> + <assert_contents> + <has_n_lines n="34"/> + <has_n_columns sep="," n="16"/> + </assert_contents> + </element> + <element name="test2_sirius" ftype="mgf"> + <assert_contents> + <has_n_lines n="54406"/> + <has_text text="BEGIN IONS"/> + </assert_contents> + </element> + </output_collection> + <assert_stderr> + <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 with localdb in batch, but user does not provide one--> + <!-- <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> --> </tests> <help><![CDATA[ MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. @@ -102,6 +152,13 @@ - Input spectra in mzml format - Spectra libraries in mgf or json format (optional) + If the batch file contains steps requiring input data sets these need to be provided + via the optional inputs. Currently this is: + + - 'Local database' for a 'Custom database search' (LocalCSVDatabaseSearchModule) step + + Please open an issue if inputs for other steps are needed: https://github.com/galaxyproject/tools-iuc/issues/new + **Outputs** Galaxy will store all outputs of MZMine in a single collection. When specifying the batch XML @@ -126,4 +183,4 @@ <citations> <citation type="doi">10.1038/s41587-023-01690-2</citation> </citations> -</tool> \ No newline at end of file +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/set_path.py Fri Nov 10 14:20:45 2023 +0000 @@ -0,0 +1,31 @@ +import argparse +import re +import sys +from xml.etree import ElementTree + +parser = argparse.ArgumentParser( + prog="set_path.py", description="update paths in mzmine batch XML" +) +parser.add_argument("--input", help="input XML") +parser.add_argument("--output", help="output XML") +parser.add_argument("--localdb", required=False, help="Local CVS DB for Search") +args = parser.parse_args() + +PATHSEP = re.compile(r"[/\\]") +tree = ElementTree.parse(args.input) + +for batchstep in tree.findall(".//batchstep"): + method = batchstep.attrib.get("method") + for current_file in batchstep.findall(".//current_file"): + if ( + method + == "io.github.mzmine.modules.dataprocessing.id_localcsvsearch.LocalCSVDatabaseSearchModule" + ): + if args.localdb: + current_file.text = args.localdb + else: + sys.exit("Batch file contains LocalCSVDatabaseSearchModule but no local DB CSV file given") + else: + current_file.text = f"./output/{PATHSEP.split(current_file.text)[-1]}" + +tree.write(args.output)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GNPS-FAULKNERLEGACY.json Fri Nov 10 14:20:45 2023 +0000 @@ -0,0 +1,8425 @@ +[ + { + "spectrum_id": "CCMSLIB00000081017", + "source_file": "B03A18.mgf", + "task": "fcad7f4133ee4a0b95bc89e8370106d9", + "scan": "1", + "ms_level": "2", + "library_membership": "GNPS-FAULKNERLEGACY", + "spectrum_status": "1", + "peaks_json": 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"Instrument": "qTof", + "PI": "Sirenas Marine Discovery", + "Data_Collector": "Sirenas Marine Discovery", + "Adduct": "M+H", + "Scan": "-1", + "Precursor_MZ": "713.846", + "ExactMass": "0.0", + "Charge": "1", + "CAS_Number": "N/A", + "Pubmed_ID": "N/A", + "Smiles": "N/A", + "INCHI": "N/A", + "INCHI_AUX": "N/A", + "Library_Class": "3", + "SpectrumID": "CCMSLIB00000081018", + "Ion_Mode": "Positive", + "create_time": "2014-05-18 17:49:45.0", + "task_id": "fcad7f4133ee4a0b95bc89e8370106d9", + "user_id": "mwang87" + } + ] + }, + { + "spectrum_id": "CCMSLIB00000081019", + "source_file": "Smenochromenes_B.mgf", + "task": "fcad7f4133ee4a0b95bc89e8370106d9", + "scan": "1", + "ms_level": "2", + "library_membership": "GNPS-FAULKNERLEGACY", + "spectrum_status": "1", + "peaks_json": 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"Instrument": "qTof", + "PI": "Sirenas Marine Discovery", + "Data_Collector": "Sirenas Marine Discovery", + "Adduct": "M+H", + "Scan": "-1", + "Precursor_MZ": "343.239", + "ExactMass": "0.0", + "Charge": "1", + "CAS_Number": "N/A", + "Pubmed_ID": "N/A", + "Smiles": "N/A", + "INCHI": "N/A", + "INCHI_AUX": "N/A", + "Library_Class": "3", + "SpectrumID": "CCMSLIB00000081143", + "Ion_Mode": "Positive", + "create_time": "2014-05-18 17:49:45.0", + "task_id": "fcad7f4133ee4a0b95bc89e8370106d9", + "user_id": "mwang87" + } + ] + } +] \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/local_database.csv Fri Nov 10 14:20:45 2023 +0000 @@ -0,0 +1,2 @@ +compound;rt;mz +test;4.0;176.0321
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_localdatabase.xml Fri Nov 10 14:20:45 2023 +0000 @@ -0,0 +1,674 @@ +<?xml version="1.0" encoding="UTF-8"?><batch mzmine_version="3.5.5"> + <batchstep method="io.github.mzmine.modules.io.import_rawdata_all.AllSpectralDataImportModule" parameter_version="1"> + <parameter name="File names"> + <file>/tmp/mzminetest/DOM_a.mzML</file> + <file>/tmp/mzminetest/DOM_b.mzXML</file> + </parameter> + <parameter name="Advanced import" selected="false"> + <parameter name="Scan filters" selected="false"> + <parameter name="Scan number"/> + <parameter name="Base Filtering Integer"/> + <parameter name="Retention time"/> + <parameter name="Mobility"/> + <parameter name="MS level filter" selected="All MS levels">1</parameter> + <parameter name="Scan definition"/> + <parameter name="Polarity">Any</parameter> + <parameter name="Spectrum type">ANY</parameter> + </parameter> + <parameter name="Crop MS1 m/z" selected="false"/> + <parameter name="MS1 detector (Advanced)" selected="false" selected_item="Centroid"> + <module name="Factor of lowest signal"> + <parameter name="Noise factor">3.0</parameter> + </module> + <module name="Centroid"> + <parameter name="Noise level">3000.0</parameter> + <parameter name="Detect isotope signals below noise level" selected="false"> + <parameter name="Chemical elements">H,C,N,O,S</parameter> + <parameter name="m/z tolerance"> + <absolutetolerance>0.0015</absolutetolerance> + <ppmtolerance>3.0</ppmtolerance> + </parameter> + <parameter name="Maximum charge of isotope m/z">2</parameter> + </parameter> + </module> + <module name="Exact mass"> + <parameter name="Noise level">1000.0</parameter> + <parameter name="Detect isotope signals below noise level" selected="false"> + <parameter name="Chemical elements">H,C,N,O,S</parameter> + <parameter name="m/z tolerance"> + <absolutetolerance>0.0015</absolutetolerance> + <ppmtolerance>3.0</ppmtolerance> + </parameter> + <parameter name="Maximum charge of isotope m/z">2</parameter> + </parameter> + </module> + <module name="Local maxima"> + <parameter name="Noise level"/> + </module> + <module name="Recursive threshold"> + <parameter name="Noise level"/> + <parameter name="Min m/z peak width"/> + <parameter name="Max m/z peak width"/> + </module> + <module name="Wavelet transform"> + <parameter name="Noise level"/> + <parameter name="Scale level"/> + <parameter name="Wavelet window size (%)"/> + </module> + <module name="Auto"> + <parameter name="Noise level">1000.0</parameter> + <parameter name="Detect isotope signals below noise level" selected="false"> + <parameter name="Chemical elements">H,C,N,O,S</parameter> + <parameter name="m/z tolerance"> + <absolutetolerance>0.0015</absolutetolerance> + <ppmtolerance>3.0</ppmtolerance> + </parameter> + <parameter name="Maximum charge of isotope m/z">2</parameter> + </parameter> + </module> + </parameter> + <parameter name="MS2 detector (Advanced)" selected="false" selected_item="Centroid"> + <module name="Factor of lowest signal"> + <parameter name="Noise factor">3.0</parameter> + </module> + <module name="Centroid"> + <parameter name="Noise level">3000.0</parameter> + <parameter name="Detect isotope signals below noise level" selected="false"> + <parameter name="Chemical elements">H,C,N,O,S</parameter> + <parameter name="m/z tolerance"> + <absolutetolerance>0.0015</absolutetolerance> + <ppmtolerance>3.0</ppmtolerance> + </parameter> + <parameter name="Maximum charge of isotope m/z">2</parameter> + </parameter> + </module> + <module name="Exact mass"> + <parameter name="Noise level">1000.0</parameter> + <parameter name="Detect isotope signals below noise level" selected="false"> + <parameter name="Chemical elements">H,C,N,O,S</parameter> + <parameter name="m/z tolerance"> + <absolutetolerance>0.0015</absolutetolerance> + <ppmtolerance>3.0</ppmtolerance> + </parameter> + <parameter name="Maximum charge of isotope m/z">2</parameter> + </parameter> 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name="Weight for m/z">3.0</parameter> + <parameter name="Retention time tolerance" unit="MINUTES">0.1</parameter> + <parameter name="Weight for RT">1.0</parameter> + <parameter name="Mobility tolerance" selected="false">1.0</parameter> + <parameter name="Mobility weight">0.0</parameter> + <parameter name="Require same charge state">false</parameter> + <parameter name="Require same ID">false</parameter> + <parameter name="Compare isotope pattern" selected="false"> + <parameter name="Isotope m/z tolerance"> + <absolutetolerance>0.001</absolutetolerance> + <ppmtolerance>5.0</ppmtolerance> + </parameter> + <parameter name="Minimum absolute intensity">0.0</parameter> + <parameter name="Minimum score">0.0</parameter> + </parameter> + <parameter name="Compare spectra similarity" selected="false"> + <parameter name="Spectral m/z tolerance"> + <absolutetolerance>0.001</absolutetolerance> + <ppmtolerance>10.0</ppmtolerance> + </parameter> + <parameter name="MS level">2</parameter> + <parameter name="Compare spectra similarity" selected_item="Weighted cosine similarity"> + <module name="Weighted cosine similarity"> + <parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter> + <parameter name="Minimum cos similarity">0.65</parameter> + <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter> + </module> + <module name="Composite cosine identity (e.g., GC-EI-MS; similar to NIST search)"> + <parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter> + <parameter name="Minimum cos similarity">0.7</parameter> + <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter> + </module> + </parameter> + </parameter> + <parameter name="Original feature list">KEEP</parameter> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.group_metacorrelate.corrgrouping.CorrelateGroupingModule" parameter_version="2"> + <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> + <parameter name="RT tolerance" unit="MINUTES">0.055000003</parameter> + <parameter name="Minimum feature height">0.0</parameter> + <parameter name="Intensity threshold for correlation">30000.0</parameter> + <parameter name="Min samples filter"> + <parameter name="Min samples in all"> + <abs>2</abs> + <rel>0.0</rel> + </parameter> + <parameter name="Min samples in group"> + <abs>0</abs> + <rel>0.0</rel> + </parameter> + <parameter name="Min %-intensity overlap">0.6</parameter> + <parameter name="Exclude gap-filled features">true</parameter> + </parameter> + <parameter name="Feature shape correlation" selected="true"> + <parameter name="Min data points">5</parameter> + <parameter name="Min data points on edge">2</parameter> + <parameter name="Measure">PEARSON</parameter> + <parameter name="Min feature shape correlation">0.85</parameter> + <parameter name="Min total correlation" selected="false">0.5</parameter> + </parameter> + <parameter name="Feature height correlation" selected="true"> + <parameter name="Minimum samples">2</parameter> + <parameter name="Measure">PEARSON</parameter> + <parameter name="Min correlation">0.7</parameter> + </parameter> + <parameter name="Suffix (or auto)" selected="false"/> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.id_ion_identity_networking.ionidnetworking.IonNetworkingModule" parameter_version="1"> + <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> + <parameter name="m/z tolerance (intra-sample)"> + <absolutetolerance>0.0015</absolutetolerance> + <ppmtolerance>3.0</ppmtolerance> + </parameter> + <parameter name="Check">ALL FEATURES</parameter> + <parameter name="Min height">0.0</parameter> + <parameter name="Ion identity library"> + <parameter name="MS mode">POSITIVE</parameter> + <parameter name="Maximum charge">2</parameter> + <parameter name="Maximum molecules/cluster">2</parameter> + <parameter name="Adducts"> + <adduct_type selected="false"> + <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="1" mass_difference="-5.4858E-4" mol_formula="" name="e" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="true"> + <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="true"> + <subpart charge="1" mass_difference="22.989218" mol_formula="Na" name="Na" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="true"> + <subpart charge="1" mass_difference="38.963158" mol_formula="K" name="K" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="true"> + <subpart charge="1" mass_difference="18.033823" mol_formula="NH4" name="NH4" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="1" mass_difference="-5.4858E-4" mol_formula="" name="e" type="ADDUCT"/> + <subpart charge="1" mass_difference="-5.4858E-4" mol_formula="" name="e" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="true"> + <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/> + <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="2" mass_difference="39.96149382" mol_formula="Ca" name="Ca" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="2" mass_difference="55.93384" mol_formula="Fe" name="Fe" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="2" mass_difference="47.96953482" mol_formula="Mg" name="Mg" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/> + <subpart charge="1" mass_difference="22.989218" mol_formula="Na" name="Na" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/> + <subpart charge="1" mass_difference="18.033823" mol_formula="NH4" name="NH4" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/> + <subpart charge="1" mass_difference="38.963158" mol_formula="K" name="K" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="true"> + <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/> + <subpart charge="1" mass_difference="22.989218" mol_formula="Na" name="Na" type="ADDUCT"/> + <subpart charge="1" mass_difference="22.989218" mol_formula="Na" name="Na" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="2" mass_difference="39.96149382" mol_formula="Ca" name="Ca" type="ADDUCT"/> + <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="2" mass_difference="55.93384" mol_formula="Fe" name="Fe" type="ADDUCT"/> + <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="1" mass_difference="0.0" mol_formula="" name="e" type="ADDUCT"/> + </adduct_type> + <adduct_type selected="false"> + <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/> + <subpart charge="2" mass_difference="47.96953482" mol_formula="Mg" name="Mg" type="ADDUCT"/> + </adduct_type> + <modification_type selected="true"> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="true"> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="-17.026549" mol_formula="NH3" name="NH3" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="15.99491462" mol_formula="O" name="O" type="CLUSTER"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="-27.994915" mol_formula="CO" name="CO" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="-43.989829" mol_formula="CO2" name="CO2" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="-28.031301" mol_formula="C2H4" name="C2H4" type="NEUTRAL_LOSS"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="46.005479" mol_formula="CHOOH" name="HFA" type="CLUSTER"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="60.021129" mol_formula="CH3COOH" name="HAc" type="CLUSTER"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="32.026215" mol_formula="CH3OH" name="MeOH" type="CLUSTER"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="41.026549" mol_formula="CH3CN" name="ACN" type="CLUSTER"/> + </modification_type> + <modification_type selected="false"> + <subpart charge="0" mass_difference="60.058064" mol_formula="C3H8O" name="IsoProp" type="CLUSTER"/> + </modification_type> + </parameter> + </parameter> + <parameter name="Annotation refinement" selected="true"> + <parameter name="Minimum size" selected="false">3</parameter> + <parameter name="Delete small networks without major ion">true</parameter> + <parameter name="Delete smaller networks: Link threshold" selected="true">4</parameter> + <parameter name="Delete networks without monomer">true</parameter> + <parameter name="Delete rows witout ion id">false</parameter> + </parameter> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.id_localcsvsearch.LocalCSVDatabaseSearchModule" parameter_version="1"> + <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> + <parameter name="Database file"> + <current_file>/tmp/mzminetest/local_database.csv</current_file> + </parameter> + <parameter name="Field separator">;</parameter> + <parameter name="Columns"> + <importtype column="neutral mass" datatype="io.github.mzmine.datamodel.features.types.numbers.NeutralMassType" selected="false"/> + <importtype column="mz" datatype="io.github.mzmine.datamodel.features.types.numbers.PrecursorMZType" selected="true"/> + <importtype column="rt" datatype="io.github.mzmine.datamodel.features.types.numbers.RTType" selected="true"/> + <importtype column="formula" datatype="io.github.mzmine.datamodel.features.types.annotations.formula.FormulaType" selected="false"/> + <importtype column="smiles" datatype="io.github.mzmine.datamodel.features.types.annotations.SmilesStructureType" selected="false"/> + <importtype column="inchi" datatype="io.github.mzmine.datamodel.features.types.annotations.InChIStructureType" selected="false"/> + <importtype column="inchi key" datatype="io.github.mzmine.datamodel.features.types.annotations.InChIKeyStructureType" selected="false"/> + <importtype column="compound" datatype="io.github.mzmine.datamodel.features.types.annotations.CompoundNameType" selected="true"/> + <importtype column="CCS" datatype="io.github.mzmine.datamodel.features.types.numbers.CCSType" selected="false"/> + <importtype column="mobility" datatype="io.github.mzmine.datamodel.features.types.numbers.MobilityType" selected="false"/> + <importtype column="comment" datatype="io.github.mzmine.datamodel.features.types.annotations.CommentType" selected="false"/> + <importtype column="adduct" datatype="io.github.mzmine.datamodel.features.types.annotations.iin.IonAdductType" selected="false"/> + <importtype column="PubChemCID" datatype="io.github.mzmine.modules.dataprocessing.id_localcsvsearch.PubChemIdType" selected="false"/> + </parameter> + <parameter name="m/z tolerance"> + <absolutetolerance>0.001</absolutetolerance> + <ppmtolerance>5.0</ppmtolerance> + </parameter> + <parameter name="Retention time tolerance" unit="MINUTES">0.2</parameter> + <parameter name="Mobility time tolerance">0.01</parameter> + <parameter name="CCS tolerance (%)">0.05</parameter> + <parameter name="Use adducts" selected="false"> + <parameter name="MS mode">POSITIVE</parameter> + <parameter name="Maximum charge">2</parameter> + <parameter name="Maximum molecules/cluster">3</parameter> + <parameter name="Adducts"/> + </parameter> + <parameter name="Filter filename header" selected="false">raw_filename</parameter> + <parameter name="Append comment fields"/> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.id_spectral_library_match.SpectralLibrarySearchModule" parameter_version="2"> + <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> + <parameter name="Spectral libraries" type="ALL_IMPORTED"/> + <parameter name="Scans for matching">MS level ≥ 2 (merged)</parameter> + <parameter name="Precursor m/z tolerance"> + <absolutetolerance>0.01</absolutetolerance> + <ppmtolerance>20.0</ppmtolerance> + </parameter> + <parameter name="Spectral m/z tolerance"> + <absolutetolerance>0.01</absolutetolerance> + <ppmtolerance>20.0</ppmtolerance> + </parameter> + <parameter name="Remove precursor">true</parameter> + <parameter name="Minimum matched signals">4</parameter> + <parameter name="Similarity" selected_item="Weighted cosine similarity"> + <module name="Weighted cosine similarity"> + <parameter name="Weights">SQRT (mz^0 * I^0.5)</parameter> + <parameter name="Minimum cos similarity">0.1</parameter> + <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter> + </module> + <module name="Composite cosine identity (e.g., GC-EI-MS; similar to NIST search)"> + <parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter> + <parameter name="Minimum cos similarity">0.7</parameter> + <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter> + </module> + </parameter> + <parameter name="Advanced" selected="false"> + <parameter name="Retention time tolerance" selected="false"/> + <parameter name="CCS tolerance [%]" selected="false">0.05</parameter> + <parameter name="13C deisotoping" selected="false"> + <parameter name="m/z tolerance"> + <absolutetolerance>0.001</absolutetolerance> + <ppmtolerance>5.0</ppmtolerance> + </parameter> + <parameter name="Monotonic shape">false</parameter> + <parameter name="Maximum charge">1</parameter> + </parameter> + <parameter name="Min matched isotope signals" selected="false">3</parameter> + <parameter name="Crop spectra to m/z overlap">false</parameter> + </parameter> + </batchstep> + <batchstep method="io.github.mzmine.modules.io.export_features_gnps.fbmn.GnpsFbmnExportAndSubmitModule" parameter_version="2"> + <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> + <parameter name="Filename"> + <current_file>/tmp/mzminetest/test2_iimn_gnps</current_file> + </parameter> + <parameter name="Merge MS/MS (experimental)" selected="false"> + <parameter name="Select spectra to merge">across samples</parameter> + <parameter name="m/z merge mode">weighted average (remove outliers)</parameter> + <parameter name="intensity merge mode">sum intensities</parameter> + <parameter name="Expected mass deviation"> + <absolutetolerance>0.001</absolutetolerance> + <ppmtolerance>5.0</ppmtolerance> + </parameter> + <parameter name="Cosine threshold (%)">0.7</parameter> + <parameter name="Signal count threshold (%)">0.2</parameter> + <parameter name="Isolation window offset (m/z)">0.0</parameter> + <parameter name="Isolation window width (m/z)">3.0</parameter> + </parameter> + <parameter name="Filter rows">MS2 OR ION IDENTITY</parameter> + <parameter name="Feature intensity">Area</parameter> + <parameter name="CSV export">SIMPLE</parameter> + <parameter name="Submit to GNPS" selected="false"> + <parameter name="Meta data file" selected="false"/> + <parameter name="Export ion identity networks">true</parameter> + <parameter name="Presets">HIGHRES</parameter> + <parameter name="Job title"/> + <parameter name="Email"/> + <parameter name="Username"/> + <parameter name="Password"/> + <parameter name="Open website">true</parameter> + </parameter> + <parameter name="Open folder">false</parameter> + </batchstep> + <batchstep method="io.github.mzmine.modules.io.export_features_sirius.SiriusExportModule" parameter_version="1"> + <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> + <parameter name="Filename"> + <current_file>D:\tmp\export_mzmine3\test2_sirius.MGF</current_file> + <last_file>D:\tmp\new_sirius\merged_new_sirius.mgf</last_file> + <last_file>D:\tmp\test\merged_new_sirius.mgf</last_file> + </parameter> + <parameter name="Merge MS/MS" selected="false"> + <parameter name="Select spectra to merge">across samples</parameter> + <parameter name="m/z merge mode">weighted average (remove outliers)</parameter> + <parameter name="intensity merge mode">sum intensities</parameter> + <parameter name="Expected mass deviation"> + <absolutetolerance>0.001</absolutetolerance> + <ppmtolerance>5.0</ppmtolerance> + </parameter> + <parameter name="Cosine threshold (%)">0.7</parameter> + <parameter name="Signal count threshold (%)">0.2</parameter> + <parameter name="Isolation window offset (m/z)">0.0</parameter> + <parameter name="Isolation window width (m/z)">3.0</parameter> + </parameter> + <parameter name="m/z tolerance"> + <absolutetolerance>0.002</absolutetolerance> + <ppmtolerance>5.0</ppmtolerance> + </parameter> + <parameter name="Only rows with annotation">false</parameter> + <parameter name="Exclude multiple charge">false</parameter> + <parameter name="Exclude multimers">false</parameter> + </batchstep> +</batch>