| Next changeset 1:90d60c9da21e (2023-11-10) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd |
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added:
mzmine_batch.xml test-data/test_small.xml |
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| diff -r 000000000000 -r 02e802817d48 mzmine_batch.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzmine_batch.xml Sat Oct 21 10:29:31 2023 +0000 |
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| @@ -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 |
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| diff -r 000000000000 -r 02e802817d48 test-data/test_small.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_small.xml Sat Oct 21 10:29:31 2023 +0000 |
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| b'@@ -0,0 +1,637 @@\n+<?xml version="1.0" encoding="UTF-8"?><batch mzmine_version="3.5.5">\r\n+ <batchstep method="io.github.mzmine.modules.io.import_rawdata_all.AllSpectralDataImportModule" parameter_version="1">\r\n+ <parameter name="File names">\r\n+ <file>/tmp/mzminetest/DOM_a.mzML</file>\r\n+ <file>/tmp/mzminetest/DOM_b.mzXML</file>\r\n+ </parameter>\r\n+ <parameter name="Advanced import" selected="false">\r\n+ <parameter name="Scan filters" selected="false">\r\n+ <parameter name="Scan number"/>\r\n+ <parameter name="Base Filtering Integer"/>\r\n+ <parameter name="Retention time"/>\r\n+ <parameter name="Mobility"/>\r\n+ <parameter name="MS level filter" selected="All MS levels">1</parameter>\r\n+ <parameter name="Scan definition"/>\r\n+ <parameter name="Polarity">Any</parameter>\r\n+ <parameter name="Spectrum type">ANY</parameter>\r\n+ </parameter>\r\n+ <parameter name="Crop MS1 m/z" selected="false"/>\r\n+ <parameter name="MS1 detector (Advanced)" selected="false" selected_item="Centroid">\r\n+ <module name="Factor of lowest signal">\r\n+ <parameter name="Noise factor">3.0</parameter>\r\n+ </module>\r\n+ <module name="Centroid">\r\n+ <parameter name="Noise level">3000.0</parameter>\r\n+ <parameter name="Detect isotope signals below noise level" selected="false">\r\n+ <parameter name="Chemical elements">H,C,N,O,S</parameter>\r\n+ <parameter name="m/z tolerance">\r\n+ <absolutetolerance>0.0015</absolutetolerance>\r\n+ <ppmtolerance>3.0</ppmtolerance>\r\n+ </parameter>\r\n+ <parameter name="Maximum charge of isotope m/z">2</parameter>\r\n+ </parameter>\r\n+ </module>\r\n+ <module name="Exact mass">\r\n+ <parameter name="Noise level">1000.0</parameter>\r\n+ <parameter name="Detect isotope signals below noise level" selected="false">\r\n+ <parameter name="Chemical elements">H,C,N,O,S</parameter>\r\n+ <parameter name="m/z tolerance">\r\n+ <absolutetolerance>0.0015</absolutetolerance>\r\n+ <ppmtolerance>3.0</ppmtolerance>\r\n+ </parameter>\r\n+ <parameter name="Maximum charge of isotope m/z">2</parameter>\r\n+ </parameter>\r\n+ </module>\r\n+ <module name="Local maxima">\r\n+ <parameter name="Noise level"/>\r\n+ </module>\r\n+ <module name="Recursive threshold">\r\n+ <parameter name="Noise level"/>\r\n+ <parameter name="Min m/z peak width"/>\r\n+ <parameter name="Max m/z peak width"/>\r\n+ </module>\r\n+ <module name="Wavelet transform">\r\n+ <parameter name="Noise level"/>\r\n+ <parameter name="Scale level"/>\r\n+ <parameter name="Wavelet window size (%)"/>\r\n+ </module>\r\n+ <module name="Auto">\r\n+ <parameter name="Noise level">1000.0</parameter>\r\n+ <parameter name="Detect isotope signals below noise level" selected="false">\r\n+ <parameter name="Chemical elements">H,C,N,O,S</parameter>\r\n+ <parameter name="m/z tolerance">\r\n+ <absolutetolerance>0.0015</absolutetolerance>\r\n+ <ppmtolerance>3.0</ppmtolerance>\r\n+ </parameter>\r\n+ <parameter name="Maximum charge of isotope m/z">2</parameter>\r\n+ </paramet'..b' <parameter name="Maximum charge">1</parameter>\r\n+ </parameter>\r\n+ <parameter name="Min matched isotope signals" selected="false">3</parameter>\r\n+ <parameter name="Crop spectra to m/z overlap">false</parameter>\r\n+ </parameter>\r\n+ </batchstep>\r\n+ <batchstep method="io.github.mzmine.modules.io.export_features_gnps.fbmn.GnpsFbmnExportAndSubmitModule" parameter_version="2">\r\n+ <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>\r\n+ <parameter name="Filename">\r\n+\t\t<current_file>/tmp/mzminetest/test2_iimn_gnps</current_file>\r\n+ </parameter>\r\n+ <parameter name="Merge MS/MS (experimental)" selected="false">\r\n+ <parameter name="Select spectra to merge">across samples</parameter>\r\n+ <parameter name="m/z merge mode">weighted average (remove outliers)</parameter>\r\n+ <parameter name="intensity merge mode">sum intensities</parameter>\r\n+ <parameter name="Expected mass deviation">\r\n+ <absolutetolerance>0.001</absolutetolerance>\r\n+ <ppmtolerance>5.0</ppmtolerance>\r\n+ </parameter>\r\n+ <parameter name="Cosine threshold (%)">0.7</parameter>\r\n+ <parameter name="Signal count threshold (%)">0.2</parameter>\r\n+ <parameter name="Isolation window offset (m/z)">0.0</parameter>\r\n+ <parameter name="Isolation window width (m/z)">3.0</parameter>\r\n+ </parameter>\r\n+ <parameter name="Filter rows">MS2 OR ION IDENTITY</parameter>\r\n+ <parameter name="Feature intensity">Area</parameter>\r\n+ <parameter name="CSV export">SIMPLE</parameter>\r\n+ <parameter name="Submit to GNPS" selected="false">\r\n+ <parameter name="Meta data file" selected="false"/>\r\n+ <parameter name="Export ion identity networks">true</parameter>\r\n+ <parameter name="Presets">HIGHRES</parameter>\r\n+ <parameter name="Job title"/>\r\n+ <parameter name="Email"/>\r\n+ <parameter name="Username"/>\r\n+ <parameter name="Password"/>\r\n+ <parameter name="Open website">true</parameter>\r\n+ </parameter>\r\n+ <parameter name="Open folder">false</parameter>\r\n+ </batchstep>\r\n+ <batchstep method="io.github.mzmine.modules.io.export_features_sirius.SiriusExportModule" parameter_version="1">\r\n+ <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>\r\n+ <parameter name="Filename">\r\n+ <current_file>D:\\tmp\\export_mzmine3\\test2_sirius.MGF</current_file>\r\n+ <last_file>D:\\tmp\\new_sirius\\merged_new_sirius.mgf</last_file>\r\n+ <last_file>D:\\tmp\\test\\merged_new_sirius.mgf</last_file>\r\n+ </parameter>\r\n+ <parameter name="Merge MS/MS" selected="false">\r\n+ <parameter name="Select spectra to merge">across samples</parameter>\r\n+ <parameter name="m/z merge mode">weighted average (remove outliers)</parameter>\r\n+ <parameter name="intensity merge mode">sum intensities</parameter>\r\n+ <parameter name="Expected mass deviation">\r\n+ <absolutetolerance>0.001</absolutetolerance>\r\n+ <ppmtolerance>5.0</ppmtolerance>\r\n+ </parameter>\r\n+ <parameter name="Cosine threshold (%)">0.7</parameter>\r\n+ <parameter name="Signal count threshold (%)">0.2</parameter>\r\n+ <parameter name="Isolation window offset (m/z)">0.0</parameter>\r\n+ <parameter name="Isolation window width (m/z)">3.0</parameter>\r\n+ </parameter>\r\n+ <parameter name="m/z tolerance">\r\n+ <absolutetolerance>0.002</absolutetolerance>\r\n+ <ppmtolerance>5.0</ppmtolerance>\r\n+ </parameter>\r\n+ <parameter name="Only rows with annotation">false</parameter>\r\n+ <parameter name="Exclude multiple charge">false</parameter>\r\n+ <parameter name="Exclude multimers">false</parameter>\r\n+ </batchstep>\r\n+</batch>\r\n' |