Mercurial > repos > iuc > mzmine_batch
changeset 0:02e802817d48 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
| author | iuc |
|---|---|
| date | Sat, 21 Oct 2023 10:29:31 +0000 |
| parents | |
| children | 90d60c9da21e |
| files | mzmine_batch.xml test-data/test_small.xml |
| diffstat | 2 files changed, 766 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzmine_batch.xml Sat Oct 21 10:29:31 2023 +0000 @@ -0,0 +1,129 @@ +<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="@VERSION_SUFFIX@">0</token> + </macros> + <xrefs> + <xref type="bio.tools">mzmine</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mzmine</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #import re + + mkdir -p input && + #for $i in $input + #set escaped_i = re.sub('[^\s\w\-\.]', '_', str($i.element_identifier)) + ln -s '$i' 'input/$escaped_i'.$i.ext && + echo 'input/$escaped_i'.$i.ext >> input.txt && + #end for + + #if $libraries + mkdir -p libraries && + #for $l in $libraries + #set escaped_l = re.sub('[^\s\w\-\.]', '_', str($l.element_identifier)) + ln -s '$l' 'libraries/$escaped_l'.$l.ext && + echo 'libraries/$escaped_l'.$l.ext >> libraries.txt && + #end for + #end if + ## 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 && + + mzmine + --batch 'batch.xml' + --input 'input.txt' + #if $libraries + --libraries 'libraries.txt' + #end if + --memory "\${MZMINE_MEMORY:-none}" + --temp "\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}" + --threads \${GALAXY_SLOTS:-1} +## ignored parameters +## -p,--pref <arg> preferences file +## -r,--running keep MZmine running in headless mode +## -tdfpseudoprofile Loads pseudo-profile frame spectra for tdf files +## instead of centroided spectra. +## -tsfprofile Loads profile spectra from .tsf data instead of +## centroid spectra. + ]]></command> + <inputs> + <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"/> + </inputs> + <outputs> + <collection name="output" type="list"> + <discover_datasets pattern="__name_and_ext__" directory="output"/> + </collection> + </outputs> + <tests> + <test> + <param name="batch" value="test_small.xml" ftype="xml"/> + <param name="input" value="DOM_a.mzML,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> + <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> + </test> + </tests> + <help><![CDATA[ + MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. + + This Galaxy tool allows to execute MZmine batches. That is you can create MZmine batch (XML) files thatdescribe the parameters of a MZmine analysis using the MZmine GUI + and use this to execute such an analysis on the Galaxy platform. + + **Inputs** + + - MZMine batch file in XML format. This file describes the parameters for a MZmine batch analysis. It can be generated with the MZmine GUI (preferentiall with a matching version, i.e. @TOOL_VERSION@). + - Input spectra in mzml format + - Spectra libraries in mgf or json format (optional) + + **Outputs** + + Galaxy will store all outputs of MZMine in a single collection. When specifying the batch XML + file one should pay attention to use file extensions that correspond to Galaxy datatypes + (which allows Galaxy to easily autodetect the datatype). The following extensions can be used + (lower/upper case does not matter): + + - mzml + - netcdf + - mgf + - txt + - msp + - csv + - mztab + - mztab2 (this is mzTab-m) + - json + - tabular (Galaxy's tsv implementation) + + Specific datasets from the collection can be accessed using the *Extract dataset* tool, e.g. + for further processing in Galaxy. + ]]></help> + <citations> + <citation type="doi">10.1038/s41587-023-01690-2</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_small.xml Sat Oct 21 10:29:31 2023 +0000 @@ -0,0 +1,637 @@ +<?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> + </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="Denormalize fragment scans (traps)">false</parameter> + </parameter> + <parameter name="Spectral library files"> + <file>/tmp/mzminetest/GNPS-FAULKNERLEGACY.json</file> + <!--<file>D:\Data\lib\HMDB.mgf</file>--> + </parameter> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule" parameter_version="1"> + <parameter name="Raw data files" type="BATCH_LAST_FILES"/> + <parameter name="Scan filters" selected="true"> + <parameter name="Scan number"/> + <parameter name="Base Filtering Integer"/> + <parameter name="Retention time"/> + <parameter name="Mobility"/> + <parameter name="MS level filter" selected="MS1, level = 1">1</parameter> + <parameter name="Scan definition"/> + <parameter name="Polarity">Any</parameter> + <parameter name="Spectrum type">ANY</parameter> + </parameter> + <parameter name="Scan types (IMS)">All scan types</parameter> + <parameter name="Mass detector" selected_item="Auto"> + <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">30000.0</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="Denormalize fragment scans (traps)">false</parameter> + <parameter name="Output netCDF filename (optional)" selected="false"/> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule" parameter_version="1"> + <parameter name="Raw data files" type="BATCH_LAST_FILES"/> + <parameter name="Scan filters" selected="true"> + <parameter name="Scan number"/> + <parameter name="Base Filtering Integer"/> + <parameter name="Retention time"/> + <parameter name="Mobility"/> + <parameter name="MS level filter" selected="MSn, level ≥ 2">3</parameter> + <parameter name="Scan definition"/> + <parameter name="Polarity">Any</parameter> + <parameter name="Spectrum type">ANY</parameter> + </parameter> + <parameter name="Scan types (IMS)">All scan types</parameter> + <parameter name="Mass detector" selected_item="Auto"> + <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">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> + </parameter> + <parameter name="Denormalize fragment scans (traps)">false</parameter> + <parameter name="Output netCDF filename (optional)" selected="false"/> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_adapchromatogrambuilder.ModularADAPChromatogramBuilderModule" parameter_version="1"> + <parameter name="Raw data files" type="BATCH_LAST_FILES"/> + <parameter name="Scan filters" selected="true"> + <parameter name="Scan number"/> + <parameter name="Base Filtering Integer"/> + <parameter name="Retention time"> + <min>0.5</min> + <max>10.0</max> + </parameter> + <parameter name="Mobility"/> + <parameter name="MS level filter" selected="MS1, level = 1">1</parameter> + <parameter name="Scan definition"/> + <parameter name="Polarity">Any</parameter> + <parameter name="Spectrum type">ANY</parameter> + </parameter> + <parameter name="Minimum consecutive scans">5</parameter> + <parameter name="Minimum intensity for consecutive scans">300000.0</parameter> + <parameter name="Minimum absolute height">500000.0</parameter> + <parameter name="m/z tolerance (scan-to-scan)"> + <absolutetolerance>0.002</absolutetolerance> + <ppmtolerance>10.0</ppmtolerance> + </parameter> + <parameter name="Suffix">eics</parameter> + <parameter name="Allow single scan chromatograms"/> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_chromatogramdeconvolution.minimumsearch.MinimumSearchFeatureResolverModule" parameter_version="2"> + <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> + <parameter name="Suffix">r</parameter> + <parameter name="Original feature list">KEEP</parameter> + <parameter name="MS/MS scan pairing" selected="true"> + <parameter name="MS1 to MS2 precursor tolerance (m/z)"> + <absolutetolerance>0.01</absolutetolerance> + <ppmtolerance>10.0</ppmtolerance> + </parameter> + <parameter name="Retention time filter" selected="Use feature edges" unit="MINUTES">0.05</parameter> + <parameter name="Minimum relative feature height" selected="true">0.25</parameter> + <parameter name="Minimum required signals" selected="true">1</parameter> + <parameter name="Limit by ion mobility edges">true</parameter> + <parameter name="Merge MS/MS spectra (TIMS)">false</parameter> + <parameter name="Minimum signal intensity (absolute, TIMS)" selected="false">6000.0</parameter> + <parameter name="Minimum signal intensity (relative, TIMS)" selected="false">0.01</parameter> + </parameter> + <parameter name="Dimension">Retention time</parameter> + <parameter name="Chromatographic threshold">0.8420000000000001</parameter> + <parameter name="Minimum search range RT/Mobility (absolute)">0.05</parameter> + <parameter name="Minimum relative height">0.0</parameter> + <parameter name="Minimum absolute height">500000.0</parameter> + <parameter name="Min ratio of peak top/edge">2.0</parameter> + <parameter name="Peak duration range (min/mobility)"> + <min>0.0</min> + <max>1.501</max> + </parameter> + <parameter name="Minimum scans (data points)">5</parameter> + </batchstep> + <batchstep method="io.github.mzmine.modules.dataprocessing.align_join.JoinAlignerModule" parameter_version="1"> + <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> + <parameter name="Feature list name">Aligned feature list</parameter> + <parameter name="m/z tolerance (sample-to-sample)"> + <absolutetolerance>0.0015</absolutetolerance> + <ppmtolerance>5.0</ppmtolerance> + </parameter> + <parameter 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_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>