Mercurial > repos > galaxyp > msconvert
diff msconvert_macros.xml @ 10:9d5de24e6ef7 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
| author | galaxyp |
|---|---|
| date | Sat, 23 Feb 2019 06:25:48 -0500 |
| parents | dd4ba10d0c45 |
| children | cc5ccfa8ee28 |
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--- a/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 +++ b/msconvert_macros.xml Sat Feb 23 06:25:48 2019 -0500 @@ -1,60 +1,91 @@ <macros> - <xml name="generic_requirements"> - <requirements> - <requirement type="package" version="3.0.9016">proteowizard</requirement> - </requirements> - </xml> - <token name="@VERSION@">3.0</token> + <token name="@VERSION@">3.0.19052</token> + <token name="@FULL_VERSION@">@VERSION@-089e81090</token> <xml name="msconvertCommand"> - <command interpreter="python"> + <command detect_errors="exit_code"> <![CDATA[ #import re #set $ext = $input.ext - msconvert_wrapper.py + + ## sanitize display name for use as temp filename + #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier) + #if $ext == 'wiff': - #set basename = 'absciex' - #if hasattr($input, 'display_name') - #set basename = $re.sub('\W','_',$input.display_name) + ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' && + ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' && + #elif $ext.endswith('tar'): + ln -s '$input' '${basename}' && + tar xf '${basename}' && + #set basename = $os.path.splitext($basename)[0] + #else + ln -s '$input' '${basename}' && + #end if + + #if $data_processing.precursor_refinement.use_mzrefinement + #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) + #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' + ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && + #end if + + uid=`id -u` && + gid=`id -g` && + + wine64_anyuser msconvert '${basename}' + --outdir outputs + --${output_type} + + #if $general_options.combineIonMobilitySpectra: + --combineIonMobilitySpectra + #end if + + #if $general_options.simAsSpectra: + --simAsSpectra + #end if + + #if $general_options.srmAsSpectra: + --srmAsSpectra + #end if + + #if $general_options.acceptZeroLengthSpectra: + --acceptZeroLengthSpectra + #end if + + #if $general_options.ignoreUnknownInstrumentError: + --ignoreUnknownInstrumentError + #end if + + #if $general_options.scan_summing.do_scan_summing: + --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" + #end if + + #if $general_options.multi_run_output.do_multi_run_output: + #if len($general_options.multi_run_output.run_index_set) > 0 + --runIndexSet " + #for $index in $general_options.multi_run_output.run_index_set + [${index.from},${index.to}] + #end for + " #end if - --input=${input.extra_files_path}/wiff - --input_name='${basename}.wiff - --implicit=${input.extra_files_path}/wiff_scan - --input=${input.extra_files_path}/wiff_scan - --input_name='${basename}.wiff.scan #else - --input=${input} - #if hasattr($input, 'display_name') - --input_name='${input.display_name}' - #end if + --runIndexSet $general_options.multi_run_output.runIndexSet #end if - --output=${output} - ## BEGIN_VERSION_DEFAULT - --fromextension=$ext - ## END_VERSION_DEFAULT - --toextension=${output_type} + + ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests + --stripLocationFromSourceFiles ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) + #if $data_processing.peak_picking.pick_peaks + --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" + #end if + #if $data_processing.precursor_refinement.use_mzrefinement - #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name) - #if $data_processing.precursor_refinement.input_ident.ext == 'mzid': - #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name) - #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml': - #set $input_ident_name = $re.sub('(?i)([.]?pep[.]?xml)*$','.pep.xml',$input_ident_name) - #end if - --ident=$data_processing.precursor_refinement.input_ident - --ident_name=$input_ident_name - --refinement=$output_refinement --filter "mzRefiner $input_ident_name msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels thresholdScore=$data_processing.precursor_refinement.thresholdScore thresholdValue=$data_processing.precursor_refinement.thresholdValue thresholdStep=$data_processing.precursor_refinement.thresholdStep - maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps" - #end if - - #if $data_processing.peak_picking.pick_peaks - --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" + maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1" #end if #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor" @@ -76,27 +107,27 @@ #end if #for threshold_entry in $data_processing.thresholds - --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" + --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" #end for #if $data_processing.filter_mz_windows.do_mzwindow_filter - --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" + --filter "mzWindow [$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 - --filter "ETDFilter $data_processing.etd_filtering.remove_precursor - $data_processing.etd_filtering.remove_charge_reduced - $data_processing.etd_filtering.remove_neutral_loss - $data_processing.etd_filtering.blanket_removal - $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units" + --filter "ETDFilter $data_processing.etd_filtering.remove_precursor + $data_processing.etd_filtering.remove_charge_reduced + $data_processing.etd_filtering.remove_neutral_loss + $data_processing.etd_filtering.blanket_removal + $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units" #end if #if $data_processing.ms2denoise.denoise - --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" + --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" #end if #if str($data_processing.ms2deisotope) == "true" - --filter "MS2Deisotope" + --filter "MS2Deisotope" #end if @@ -106,39 +137,38 @@ #end if #if len($filtering.indices) > 0 - --filter "index - #for $index in $filtering.indices - [${index.from},${index.to}] - #end for - " + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " #end if #if len($filtering.scan_numbers) > 0 - --filter "scanNumber - #for $scan_number in $filtering.scan_numbers - [${scan_number.from},${scan_number.to}] - #end for - " + --filter "scanNumber + #for $scan_number in $filtering.scan_numbers + [${scan_number.from},${scan_number.to}] + #end for + " #end if #if $filtering.strip_it.value - --filter "stripIT" + --filter "stripIT" #end if #if $filtering.filter_ms_levels.do_ms_level_filter - --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" + --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" #end if #if str($filtering.polarity) != "false" - --filter "polarity $filtering.polarity" + --filter "polarity $filtering.polarity" #end if #if str($filtering.analyzer) != "false" - --filter "analyzer $filtering.analyzer" + --filter "analyzer $filtering.analyzer" #end if ## OUTPUT ENCODING - -- #set $mz_encoding = str($settings.mz_encoding) #set $intensity_encoding = str($settings.intensity_encoding) #if $mz_encoding == $intensity_encoding @@ -154,28 +184,43 @@ #set binary_compression = str($settings.binary_compression) #if $binary_compression == "zlib" - --zlib + --zlib #else if $binary_compression == "numpressLinearPic" - --numpressLinear --numpressPic + --numpressLinear --numpressPic #else if $binary_compression == "numpressLinearSlof" - --numpressLinear --numpressSlof + --numpressLinear --numpressSlof #else if $binary_compression == "numpressLinear" - --numpressLinear + --numpressLinear #else if $binary_compression == "numpressPic" - --numpressPic + --numpressPic #else if $binary_compression == "numpressSlof" - --numpressSlof + --numpressSlof #end if #if $settings.gzip_compression - --gzip + --gzip #end if + #if $general_options.multi_run_output.do_multi_run_output == 'false': + --outfile '${os.path.splitext($basename)[0]}' + && sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}' + #else + && sudo chown \$uid:\$gid 'outputs' -R + && ls -la outputs/ + #end if + + #if $data_processing.precursor_refinement.use_mzrefinement + && sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement' + #end if ]]> </command> </xml> <xml name="msconvertInputParameters"> + <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses proprietary vendor libraries; to run it you must agree to the vendor licenses. Read them at http://www.proteowizard.org/licenses.html"> + <validator type="expression" message="You must agree to the vendor licenses to run msconvert.">True == value</validator> + </param> + <param name="output_type" type="select" label="Output Type"> <option value="mz5" selected="true">mz5</option> <option value="mzML">mzML</option> @@ -184,23 +229,22 @@ <option value="ms2">ms2</option> </param> - <section name="data_processing" title="Data Processing Filters"> - - <conditional name="peak_picking"> - <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> - <option value="1">MS1 Only (1)</option> - <option value="2">MS2 Only (2)</option> - <option value="2-">MS2 and on (2-)</option> - <option value="1-" selected="true">All Levels (1-)</option> - </param> - <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)"> - <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option> - <option value="cwt">CantWaiT - continuous wavelet transform</option> - </param> - </when> + <section name="data_processing" title="Data Processing Filters"> + <conditional name="peak_picking"> + <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> + <option value="1">MS1 Only (1)</option> + <option value="2">MS2 Only (2)</option> + <option value="2-">MS2 and on (2-)</option> + <option value="1-" selected="true">All Levels (1-)</option> + </param> + <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)"> + <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option> + <option value="cwt">CantWaiT - continuous wavelet transform</option> + </param> + </when> </conditional> <conditional name="precursor_refinement"> @@ -208,8 +252,18 @@ <when value="false"></when> <when value="true"> <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" /> - <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+" /> - <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10." /> + <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+"> + <sanitizer> + <valid initial="string.letters" /> + </sanitizer> + </param> + <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="-" /> + </valid> + </sanitizer> + </param> <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." /> <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" /> <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels"> @@ -369,6 +423,37 @@ </param> </section> + <section name="general_options" title="General Options"> + <param argument="--combineIonMobilitySpectra" type="boolean" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." /> + + <conditional name="scan_summing"> + <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" 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" /> + <when value="false" /> + <when value="true"> + <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." /> + <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." /> + <param name="ionMobilityTol" type="float" label="Ion mobility tolerance" value="0.01" min="0" optional="true" help="Spectra with ion mobility values with a difference less than this tolerance are summed together. Only relevant for ion mobility spectra." /> + </when> + </conditional> + + <param argument="--simAsSpectra" type="boolean" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" /> + <param argument="--srmAsSpectra" type="boolean" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" /> + <param argument="--acceptZeroLengthSpectra" type="boolean" label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" /> + <param argument="--ignoreUnknownInstrumentError" type="boolean" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" /> + + <conditional name="multi_run_output"> + <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" 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)" /> + <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)" /> + </when> + <when value="true"> + <repeat name="run_index_set" title="Select runs for multi-run sources" help="For multi-run sources (e.g. WIFF), select only the specified run indices"> + <param name="from" type="integer" label="Run Index From" value="0" min="0" optional="false" /> + <param name="to" type="integer" label="Run Index To" value="0" min="0" optional="true" /> + </repeat> + </when> + </conditional> + </section> <section name="settings" title="Output Encoding Settings"> <param type="select" name="mz_encoding" label="m/z Encoding Precision"> @@ -394,7 +479,8 @@ <xml name="msconvertOutput"> <outputs> - <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" > + <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> <change_format> <when input="output_type" value="mz5" format="mz5" /> <when input="output_type" value="mzXML" format="mzxml" /> @@ -402,9 +488,13 @@ <when input="output_type" value="mgf" format="mgf" /> </change_format> </data> - <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv"> + <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv"> <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter> </data> + <collection name="multi_run_output_list" type="list" label="${($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'] == True</filter> + <discover_datasets pattern="__name_and_ext__" directory="outputs" /> + </collection> </outputs> </xml> @@ -412,35 +502,129 @@ <xml name="msconvert_tests"> <test> <param name="input" value="small.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" /> + <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> + </test> + <test> + <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-" /> + <output name="output" file="small-peakpicking-vendor-allMS.mzML" lines_diff="4" /> + </test> + <test> + <param name="input" value="ThyroglobMRM000003.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" /> + <output name="output" file="ThyroglobMRM000003.mzML" lines_diff="4" /> + </test> + <test> + <param name="input" value="MassLynxTest.raw.tar" /> + <param name="license_agreement" value="true" /> + <param name="output_type" value="mzML" /> + <output name="output" file="MassLynxTest.mzML" lines_diff="4" /> + </test> + <test> + <param name="input" value="AgilentMassHunterTest.d.tar" /> + <param name="license_agreement" value="true" /> + <param name="output_type" value="mzXML" /> + <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" /> + </test> + <test> + <param name="input" value="BrukerBafTest.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-" /> + <output name="output" file="BrukerBafTest.mzML" lines_diff="4" /> + </test> + <test> + <param name="input" value="SciexTest.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" lines_diff="4" /> + </test> + <test> + <param name="input" value="SciexTest.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" lines_diff="4" /> + </test> + <test> + <param name="input" value="SciexTest.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" /> + <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" lines_diff="4" /> + </test> + <test> + <param name="input" value="SciexTest.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" /> + <output_collection name="multi_run_output_list" type="list"> + <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" /> + <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" /> + </output_collection> + </test> + <test> + <param name="input" value="SciexTest.wiff.tar" /> + <param name="license_agreement" value="true" /> + <param name="output_type" value="mzML" /> + <param name="do_multi_run_output" value="true" /> + <output_collection name="multi_run_output_list" type="list"> + <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" /> + <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" /> + </output_collection> </test> <!-- this data file only has profile MS1, so the result is the same --> <test> <param name="input" value="small.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" /> + <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> - <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" /> + <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-zlib-32.mzXML" lines_diff="6" /> </test> <!-- TODO: how to test gzipped output? <test> @@ -464,53 +648,60 @@ <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-numpressLP.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-numpressLS.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-numpressL.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-numpressP.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-numpressS.mzML" lines_diff="114" /> </test> <test> <param name="input" value="Rpal_01.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.gz" /> + <param name="input_ident" value="Rpal_01.pepXML" /> <param name="thresholdScore" value="mvh" /> <param name="thresholdValue" value="40-" /> <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" /> - <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> + <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> @@ -519,10 +710,11 @@ <param name="maxMultipleCharge" value="5" /> <param name="singleChargeFractionTIC" value="0.95" /> <param name="maxKnownCharge" value="8" /> - <output name="output" file="small-chargeStatePredictor.mzML" /> + <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> @@ -533,10 +725,11 @@ <param name="halfIsoWidth" value="1.5" /> <param name="defaultMinCharge" value="1" /> <param name="defaultMaxCharge" value="5" /> - <output name="output" file="small-turbocharger.mzML" /> + <output name="output" file="small-turbocharger.mzML" lines_diff="114" /> </test> <test> <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.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" /> @@ -550,6 +743,7 @@ </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> @@ -558,43 +752,48 @@ <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" /> + <output name="output" file="small-threshold.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-mzWindow.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-denoise.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-deisotope.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="activation" value="CID" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-activation.mzML" /> + <output name="output" file="small-activation.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> @@ -603,40 +802,45 @@ <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" /> + <output name="output" file="small-index-filter.mzML" lines_diff="32" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-strip-it.mzML" lines_diff="100" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> + <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <param name="license_agreement" value="true" /> <param name="output_type" value="mzML" /> <param name="polarity" value="positive" /> <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-polarity-filter.mzML" /> + <output name="output" file="small-polarity-filter.mzML" lines_diff="114" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> + <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" /> + <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.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" /> @@ -645,7 +849,7 @@ <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" /> <!-- the scan numbers here produce the same output as the index test above --> + <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above --> </test> <!--<test> <param name="input" value="small.mzML" /> @@ -657,7 +861,7 @@ <xml name="msconvert_help"> **What it does** -Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available. +Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available. You can view the original documentation here_.