Mercurial > repos > galaxyp > msconvert
diff msconvert_macros.xml @ 18:331a50e8fd2f draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
| author | galaxyp |
|---|---|
| date | Mon, 10 Mar 2025 07:48:32 +0000 |
| parents | ab6c14374bc0 |
| children |
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--- a/msconvert_macros.xml Thu Aug 15 16:19:28 2024 +0000 +++ b/msconvert_macros.xml Mon Mar 10 07:48:32 2025 +0000 @@ -1,6 +1,7 @@ <macros> <token name="@VERSION@">3.0.20287</token> <token name="@FULL_VERSION@">@VERSION@-769529fa4</token> + <token name="@PROFILE_VERSION@">24.2</token> <xml name="msconvertCommand"> <command detect_errors="exit_code"> <![CDATA[ @@ -61,7 +62,7 @@ $general_options.acceptZeroLengthSpectra $general_options.ignoreUnknownInstrumentError - #if $general_options.scan_summing.do_scan_summing: + #if $general_options.scan_summing.do_scan_summing == "true": --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" #end if @@ -81,7 +82,7 @@ --stripLocationFromSourceFiles ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) - #if $data_processing.peak_picking.pick_peaks + #if $data_processing.peak_picking.pick_peaks == "true" --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" #end if @@ -116,11 +117,11 @@ --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" #end for - #if $data_processing.filter_mz_windows.do_mzwindow_filter + #if $data_processing.filter_mz_windows.do_mzwindow_filter == "true" --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" #end if - #if $data_processing.etd_filtering.do_etd_filtering + #if $data_processing.etd_filtering.do_etd_filtering == "true" --filter "ETDFilter $data_processing.etd_filtering.remove_precursor $data_processing.etd_filtering.remove_charge_reduced $data_processing.etd_filtering.remove_neutral_loss @@ -128,7 +129,7 @@ $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units" #end if - #if $data_processing.ms2denoise.denoise + #if $data_processing.ms2denoise.denoise == "true" --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" #end if @@ -136,7 +137,7 @@ --filter "MS2Deisotope" #end if - #if $data_processing.demultiplex.demultiplex_on + #if $data_processing.demultiplex.demultiplex_on == "true" --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize" #end if @@ -165,7 +166,7 @@ --filter "stripIT" #end if - #if $filtering.filter_ms_levels.do_ms_level_filter + #if $filtering.filter_ms_levels.do_ms_level_filter == "true" --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" #end if @@ -206,7 +207,7 @@ --numpressSlof #end if - #if $settings.gzip_compression + #if $settings.gzip_compression == "true" --gzip #end if @@ -253,7 +254,7 @@ <conditional name="peak_picking"> <param type="select" name="pick_peaks" label="Apply peak picking?"> <option value="true">Yes</option> - <option value="false">No</option> + <option value="false" selected="true">No</option> </param> <when value="false" /> <when value="true"> @@ -345,7 +346,7 @@ <conditional name="filter_mz_windows"> <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help=""> <option value="true">Yes</option> - <option value="false">No</option> + <option value="false" selected="true">No</option> </param> <when value="false" /> <when value="true"> @@ -357,7 +358,7 @@ <conditional name="etd_filtering"> <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?"> <option value="true">Yes</option> - <option value="false">No</option> + <option value="false" selected="true">No</option> </param> <when value="false" /> <when value="true"> @@ -388,7 +389,7 @@ <conditional name="ms2denoise"> <param name="denoise" type="select" label="De-noise MS2 with moving window filter"> <option value="true">Yes</option> - <option value="false">No</option> + <option value="false" selected="true">No</option> </param> <when value="true"> <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" /> @@ -403,7 +404,7 @@ <conditional name="demultiplex"> <param name="demultiplex_on" type="select" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)"> <option value="true">Yes</option> - <option value="false">No</option> + <option value="false" selected="true">No</option> </param> <when value="true"> <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" /> @@ -463,7 +464,7 @@ <conditional name="filter_ms_levels"> <param name="do_ms_level_filter" type="select" label="Filter MS Levels"> <option value="true">Yes</option> - <option value="false">No</option> + <option value="false" selected="true">No</option> </param> <when value="false" /> <when value="true"> @@ -494,7 +495,7 @@ <conditional name="scan_summing"> <param name="do_scan_summing" type="select" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR"> <option value="true">Yes</option> - <option value="false">No</option> + <option value="false" selected="true">No</option> </param> <when value="false" /> <when value="true"> @@ -512,7 +513,7 @@ <conditional name="multi_run_output"> <param name="do_multi_run_output" type="select" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)"> <option value="true">Yes</option> - <option value="false">No</option> + <option value="false" selected="true">No</option> </param> <when value="false"> <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" /> @@ -551,7 +552,7 @@ <xml name="msconvertOutput"> <outputs> <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" > - <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter> + <filter>general_options['multi_run_output']['do_multi_run_output'] == "false"</filter> <change_format> <when input="output_type" value="mz5" format="mz5" /> <when input="output_type" value="mzXML" format="mzxml" /> @@ -572,29 +573,20 @@ <xml name="msconvert_tests"> <test expect_num_outputs="1"> - <param name="input" value="small.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="pick_peaks" value="true" /> - <param name="pick_peaks_algorithm" value="cwt" /> - <param name="pick_peaks_ms_levels" value="1-" /> - <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" /> - </test> - <test expect_num_outputs="1"> <param name="input" value="small.RAW" ftype="thermo.raw" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="pick_peaks" value="true" /> - <param name="pick_peaks_algorithm" value="vendor" /> - <param name="pick_peaks_ms_levels" value="1-" /> + <param name="data_processing|peak_picking|pick_peaks" value="true" /> + <param name="data_processing|peak_picking|pick_peaks_algorithm" value="vendor" /> + <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1-" /> <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" /> </test> <test expect_num_outputs="1"> <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="combineIonMobilitySpectra" value="true" /> - <param name="do_scan_summing" value="true" /> + <param name="general_options|combineIonMobilitySpectra" value="true" /> + <param name="general_options|scan_summing|do_scan_summing" value="true" /> <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" /> </test> <test expect_num_outputs="1"> @@ -613,48 +605,29 @@ <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="pick_peaks" value="true" /> - <param name="pick_peaks_algorithm" value="vendor" /> - <param name="pick_peaks_ms_levels" value="1-" /> + <param name="data_processing|peak_picking|pick_peaks" value="true" /> + <param name="data_processing|peak_picking|pick_peaks_algorithm" value="vendor" /> + <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1-" /> <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" /> </test> <test expect_num_outputs="1"> <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="do_multi_run_output" value="false" /> - <param name="runIndexSet" value="0" /> - <output name="output" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> - <param name="license_agreement" value="true" /> <param name="output_type" value="mzXML" /> - <param name="do_multi_run_output" value="false" /> - <param name="runIndexSet" value="0" /> - <param name="indices_0|from" value="0" /> - <param name="indices_0|to" value="499" /> - <param name="srmAsSpectra" value="true" /> - <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzXML" /> - <param name="do_multi_run_output" value="false" /> - <param name="runIndexSet" value="1" /> - <param name="indices_0|from" value="0" /> - <param name="indices_0|to" value="499" /> - <param name="srmAsSpectra" value="true" /> + <param name="general_options|multi_run_output|do_multi_run_output" value="false" /> + <param name="general_options|multi_run_output|runIndexSet" value="1" /> + <param name="filtering|indices_0|from" value="0" /> + <param name="filtering|indices_0|to" value="499" /> + <param name="general_options|srmAsSpectra" value="true" /> <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" /> </test> <test expect_num_outputs="1"> <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="do_multi_run_output" value="true" /> - <param name="run_index_set_0|from" value="0" /> - <param name="run_index_set_0|to" value="1" /> + <param name="general_options|multi_run_output|do_multi_run_output" value="true" /> + <param name="general_options|multi_run_output|run_index_set_0|from" value="0" /> + <param name="general_options|multi_run_output|run_index_set_0|to" value="1" /> <output_collection name="multi_run_output_list" type="list"> <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" /> @@ -664,7 +637,7 @@ <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="do_multi_run_output" value="true" /> + <param name="general_options|multi_run_output|do_multi_run_output" value="true" /> <output_collection name="multi_run_output_list" type="list"> <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" /> @@ -673,37 +646,20 @@ <!-- this data file only has profile MS1, so the result is the same --> <test expect_num_outputs="1"> - <param name="input" value="small.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="pick_peaks" value="true" /> - <param name="pick_peaks_algorithm" value="cwt" /> - <param name="pick_peaks_ms_levels" value="1" /> - <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" /> - </test> - <test expect_num_outputs="1"> <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mz5" /> - <param name="mz_encoding" value="64" /> - <param name="intensity_encoding" value="64" /> + <param name="settings|mz_encoding" value="64" /> + <param name="settings|intensity_encoding" value="64" /> <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" /> </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzXML" /> - <param name="mz_encoding" value="32" /> - <param name="intensity_encoding" value="32" /> - <output name="output" file="small-zlib-32.mzXML" ftype="mzxml" lines_diff="6" /> - </test> <!-- TODO: how to test gzipped output? <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="output_type" value="mzXML" /> <param name="mz_encoding" value="32" /> <param name="intensity_encoding" value="32" /> - <param name="binary_compression" value="false" /> + <param name="settings|binary_compression" value="false" /> <param name="gzip_compression" value="true" /> <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" /> </test> @@ -712,220 +668,126 @@ <param name="output_type" value="mzML" /> <param name="mz_encoding" value="32" /> <param name="intensity_encoding" value="32" /> - <param name="binary_compression" value="false" /> + <param name="settings|binary_compression" value="false" /> <param name="gzip_compression" value="true" /> <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" /> </test>--> - - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-numpressLP.mzML" ftype="mzml" lines_diff="114" /> - </test> - - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinearSlof" /> - <output name="output" file="small-numpressLS.mzML" ftype="mzml" lines_diff="114" /> - </test> - - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinear" /> - <output name="output" file="small-numpressL.mzML" ftype="mzml" lines_diff="114" /> - </test> - - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressPic" /> - <output name="output" file="small-numpressP.mzML" ftype="mzml" lines_diff="114" /> - </test> - - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressSlof" /> - <output name="output" file="small-numpressS.mzML" ftype="mzml" lines_diff="114" /> - </test> - - <test expect_num_outputs="1"> + <test expect_num_outputs="2"> <param name="input" value="Rpal_01.mz5" ftype="mz5" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinearPic" /> - <param name="use_mzrefinement" value="true" /> - <param name="input_ident" value="Rpal_01.pepXML" /> - <param name="thresholdScore" value="mvh" /> - <param name="thresholdValue" value="40-" /> + <param name="settings|binary_compression" value="numpressLinearPic" /> + <param name="data_processing|precursor_refinement|use_mzrefinement" value="true" /> + <param name="data_processing|precursor_refinement|input_ident" value="Rpal_01.pepXML" /> + <param name="data_processing|precursor_refinement|thresholdScore" value="mvh" /> + <param name="data_processing|precursor_refinement|thresholdValue" value="40-" /> <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" /> <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" /> </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> + <param name="input" value="small.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinearPic" /> - <param name="charge_state_calculation_method" value="predictor" /> - <param name="predictor_overrideExistingCharge" value="true" /> - <param name="minMultipleCharge" value="2" /> - <param name="maxMultipleCharge" value="5" /> - <param name="singleChargeFractionTIC" value="0.95" /> - <param name="maxKnownCharge" value="8" /> - <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" /> + + <param name="data_processing|peak_picking|pick_peaks" value="true" /> + <param name="data_processing|peak_picking|pick_peaks_algorithm" value="cwt" /> + <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1" /> + + <param name="data_processing|thresholds_0|threshold_type" value="count" /> + <param name="data_processing|thresholds_0|value" value="100" /> + <param name="data_processing|thresholds_0|orientation" value="most-intense" /> + <param name="data_processing|thresholds_1|threshold_type" value="absolute" /> + <param name="data_processing|thresholds_1|value" value="1" /> + <param name="data_processing|thresholds_1|orientation" value="most-intense" /> + + <param name="data_processing|filter_mz_windows|do_mzwindow_filter" value="true" /> + <param name="data_processing|filter_mz_windows|mz_window_from" value="420" /> + <param name="data_processing|filter_mz_windows|mz_window_to" value="840" /> + + <param name="filtering|indices_0|from" value="0" /> + <param name="filtering|indices_0|to" value="20" /> + <param name="filtering|indices_1|from" value="41" /> + <param name="filtering|indices_1|to" value="41" /> + + <param name="filtering|filter_ms_levels|do_ms_level_filter" value="true" /> + <param name="filtering|filter_ms_levels|ms_level_from" value="2" /> + <param name="filtering|filter_ms_levels|ms_level_to" value="2" /> + + <param name="filtering|scan_numbers_0|from" value="5" /> + <param name="filtering|scan_numbers_0|to" value="25" /> + <param name="filtering|scan_numbers_1|from" value="40" /> + <param name="filtering|scan_numbers_1|to" value="40" /> + + <param name="data_processing|ms2deisotope" value="true" /> + + <param name="data_processing|ms2denoise|denoise" value="true" /> + <param name="data_processing|ms2denoise|num_peaks" value="10" /> + <param name="data_processing|ms2denoise|window_width" value="40" /> + <param name="data_processing|ms2denoise|relax" value="false" /> + + <param name="data_processing|charge_state_calculation|charge_state_calculation_method" value="predictor" /> + <param name="data_processing|charge_state_calculation|predictor_overrideExistingCharge" value="true" /> + <param name="data_processing|charge_state_calculation|minMultipleCharge" value="2" /> + <param name="data_processing|charge_state_calculation|maxMultipleCharge" value="5" /> + <param name="data_processing|charge_state_calculation|singleChargeFractionTIC" value="0.95" /> + <param name="data_processing|charge_state_calculation|maxKnownCharge" value="8" /> + + <param name="settings|mz_encoding" value="32" /> + <param name="settings|intensity_encoding" value="32" /> + + <param name="settings|binary_compression" value="numpressLinearPic" /> + <output name="output" file="small-composite-test.mzML" ftype="mzml" /> </test> <test expect_num_outputs="1"> <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinearPic" /> - <param name="charge_state_calculation_method" value="turbocharger" /> - <param name="minCharge" value="1" /> - <param name="maxCharge" value="5" /> - <param name="precursorsBefore" value="1" /> - <param name="precursorsAfter" value="1" /> - <param name="halfIsoWidth" value="1.5" /> - <param name="defaultMinCharge" value="1" /> - <param name="defaultMaxCharge" value="5" /> - <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="do_etd_filtering" value="true" /> - <param name="remove_precursor" value="true" /> - <param name="remove_charge_reduced" value="true" /> - <param name="remove_neutral_loss" value="false" /> - <param name="blanket_removal" value="false" /> - <param name="matching_tolerance" value="50" /> - <param name="matching_tolerance_units" value="ppm" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" /> + <param name="settings|binary_compression" value="numpressLinearPic" /> + <param name="data_processing|charge_state_calculation|charge_state_calculation_method" value="turbocharger" /> + <param name="data_processing|charge_state_calculation|minCharge" value="1" /> + <param name="data_processing|charge_state_calculation|maxCharge" value="5" /> + <param name="data_processing|charge_state_calculation|precursorsBefore" value="1" /> + <param name="data_processing|charge_state_calculation|precursorsAfter" value="1" /> + <param name="data_processing|charge_state_calculation|halfIsoWidth" value="1.5" /> + <param name="data_processing|charge_state_calculation|defaultMinCharge" value="1" /> + <param name="data_processing|charge_state_calculation|defaultMaxCharge" value="5" /> + <param name="filtering|strip_it" value="true" /> + <output name="output" file="small-composite-test-2.mzML" ftype="mzml" /> </test> <test expect_num_outputs="1"> <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="thresholds_0|threshold_type" value="count" /> - <param name="thresholds_0|value" value="100" /> - <param name="thresholds_0|orientation" value="most-intense" /> - <param name="thresholds_1|threshold_type" value="absolute" /> - <param name="thresholds_1|value" value="1" /> - <param name="thresholds_1|orientation" value="most-intense" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-threshold.mzML" lines_diff="114" ftype="mzml" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="do_mzwindow_filter" value="true" /> - <param name="mz_window_from" value="420" /> - <param name="mz_window_to" value="840" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-mzWindow.mzML" lines_diff="114" ftype="mzml" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="denoise" value="true" /> - <param name="num_peaks" value="10" /> - <param name="window_width" value="40" /> - <param name="relax" value="false" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-denoise.mzML" lines_diff="114" ftype="mzml" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="ms2deisotope" value="true" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="activation" value="CID" /> - <param name="binary_compression" value="numpressLinearPic" /> + <param name="filtering|activation" value="CID" /> + <param name="settings|binary_compression" value="numpressLinearPic" /> <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" /> </test> <test expect_num_outputs="1"> <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="indices_0|from" value="2" /> - <param name="indices_0|to" value="4" /> - <param name="indices_1|from" value="10" /> - <param name="indices_1|to" value="10" /> - <param name="indices_2|from" value="13" /> - <param name="indices_2|to" value="15" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="strip_it" value="true" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="do_ms_level_filter" value="true" /> - <param name="ms_level_from" value="2" /> - <param name="ms_level_to" value="2" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="polarity" value="positive" /> - <param name="binary_compression" value="numpressLinearPic" /> + <param name="filtering|polarity" value="positive" /> + <param name="settings|binary_compression" value="numpressLinearPic" /> <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" /> </test> <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> + <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" /> <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> - <param name="analyzer" value="IT" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" /> - </test> - <test expect_num_outputs="1"> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> - <param name="license_agreement" value="true" /> - <param name="output_type" value="mzML" /> - <param name="scan_numbers_0|from" value="3" /> - <param name="scan_numbers_0|to" value="5" /> - <param name="scan_numbers_1|from" value="11" /> - <param name="scan_numbers_1|to" value="11" /> - <param name="scan_numbers_2|from" value="14" /> - <param name="scan_numbers_2|to" value="16" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-index-filter.mzML" lines_diff="86" ftype="mzml"/> <!-- the scan numbers here produce the same output as the index test above --> + <param name="data_processing|etd_filtering|do_etd_filtering" value="true" /> + <param name="data_processing|etd_filtering|remove_precursor" value="true" /> + <param name="data_processing|etd_filtering|remove_charge_reduced" value="true" /> + <param name="data_processing|etd_filtering|remove_neutral_loss" value="false" /> + <param name="data_processing|etd_filtering|blanket_removal" value="false" /> + <param name="data_processing|etd_filtering|matching_tolerance" value="50" /> + <param name="data_processing|etd_filtering|matching_tolerance_units" value="PPM" /> + <param name="settings|binary_compression" value="numpressLinearPic" /> + <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" /> </test> <!--<test> <param name="input" value="small.mzML" /> <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinearPic" /> + <param name="settings|binary_compression" value="numpressLinearPic" /> <output name="output" file="small-deisotope-poisson.mzML" /> </test>--> </xml>