Mercurial > repos > galaxyp > msconvert
changeset 11:cc5ccfa8ee28 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d
| author | galaxyp |
|---|---|
| date | Thu, 28 Feb 2019 14:14:44 -0500 |
| parents | 9d5de24e6ef7 |
| children | 9ec469ff191a |
| files | msconvert_macros.xml msconvert_macros.xml.orig |
| diffstat | 2 files changed, 14 insertions(+), 900 deletions(-) [+] |
line wrap: on
line diff
--- a/msconvert_macros.xml Sat Feb 23 06:25:48 2019 -0500 +++ b/msconvert_macros.xml Thu Feb 28 14:14:44 2019 -0500 @@ -9,19 +9,30 @@ #set $ext = $input.ext ## sanitize display name for use as temp filename - #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier) + #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier) #if $ext == 'wiff': ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' && ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' && + #set inputmask = "'"+$basename+"'" #elif $ext.endswith('tar'): ln -s '$input' '${basename}' && tar xf '${basename}' && #set basename = $os.path.splitext($basename)[0] + #if $ext.startswith('waters'): + #set inputmask = '*.raw' + #elif $ext.startswith('agilent') or $ext.startswith('bruker'): + #set inputmask = '*.d' + #elif $ext.startswith('wiff'): + #set inputmask = '*.wiff *.wiff2' + #else + #raise RuntimeError("Unrecognized type of tar (${ext})") + #end if #else ln -s '$input' '${basename}' && + #set inputmask = "'"+$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' @@ -31,7 +42,7 @@ uid=`id -u` && gid=`id -g` && - wine64_anyuser msconvert '${basename}' + wine64_anyuser msconvert ${inputmask} --outdir outputs --${output_type}
--- a/msconvert_macros.xml.orig Sat Feb 23 06:25:48 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,897 +0,0 @@ -<macros> - <token name="@VERSION@">3.0.19052</token> - <token name="@FULL_VERSION@">@VERSION@-089e81090</token> - - <xml name="msconvertCommand"> - <command detect_errors="exit_code"> -<![CDATA[ - #import re - #set $ext = $input.ext - - ## sanitize display name for use as temp filename - #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier) - - #if $ext == 'wiff': - ln -s '${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 - #else - --runIndexSet $general_options.multi_run_output.runIndexSet - #end if - - ## 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 - --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 assumeHighRes=1" - #end if - - #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor" - --filter "chargeStatePredictor - overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge - minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge - maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge - singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC - maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge" - #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger" - --filter "turbocharger - minCharge=$data_processing.charge_state_calculation.minCharge - maxCharge=$data_processing.charge_state_calculation.maxCharge - precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore - precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter - halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth - defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge - defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge" - #end if - - #for threshold_entry in $data_processing.thresholds - --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]" - #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" - #end if - - #if $data_processing.ms2denoise.denoise - --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" - #end if - - - ## SCAN INCLUSION/EXCLUSION FILTERS - #if str($filtering.activation) != "false" - --filter "activation $filtering.activation" - #end if - - #if len($filtering.indices) > 0 - --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 - " - #end if - - #if $filtering.strip_it.value - --filter "stripIT" - #end if - - #if $filtering.filter_ms_levels.do_ms_level_filter - --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" - #end if - - #if str($filtering.polarity) != "false" - --filter "polarity $filtering.polarity" - #end if - - #if str($filtering.analyzer) != "false" - --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 - #if $mz_encoding == "64" - --64 - #else - --32 - #end if - #else - --mz${mz_encoding} - --inten${intensity_encoding} - #end if - - #set binary_compression = str($settings.binary_compression) - #if $binary_compression == "zlib" - --zlib - #else if $binary_compression == "numpressLinearPic" - --numpressLinear --numpressPic - #else if $binary_compression == "numpressLinearSlof" - --numpressLinear --numpressSlof - #else if $binary_compression == "numpressLinear" - --numpressLinear - #else if $binary_compression == "numpressPic" - --numpressPic - #else if $binary_compression == "numpressSlof" - --numpressSlof - #end if - - #if $settings.gzip_compression - --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'/* - && 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"> -<<<<<<< HEAD - <option value="mz5" selected="true">mz5</option> - <option value="mzml">mzML</option> - <option value="mzxml">mzXML</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> -======= - <option value="mz5" selected="true">mz5</option> - <option value="mzML">mzML</option> - <option value="mzXML">mzXML</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> ->>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213 - </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> - </conditional> - - <conditional name="precursor_refinement"> - <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" /> - <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+"> - <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"> - <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> - </when> - </conditional> - - <conditional name="charge_state_calculation"> - <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?"> - <option value="false">no</option> - <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option> - <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option> - </param> - <when value="false" /> - <when value="predictor"> - <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" /> - <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" /> - <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" /> - <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" /> - <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for "known" charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" /> - </when> - <when value="turbocharger"> - <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." /> - <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." /> - <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" /> - <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" /> - <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" /> - <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" /> - <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" /> - </when> - </conditional> - - <repeat name="thresholds" title="Filter by Threshold"> - <param type="select" label="Specify threshold on" name="threshold_type" help=""> - <option value="count">Peak count</option> - <option value="count-after-ties">Peak count (after ties)</option> - <option value="absolute">Peak absolute intensity</option> - <option value="bpi-relative">Fraction of base peak intensity</option> - <option value="tic-relative">Fraction of total ion current</option> - <option value="tic-fraction">Aggregate fraction of total ion current</option> - </param> - <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the "Aggregated fraction" method, peaks are accepted until this fraction of the TIC is accounted for." /> - <param type="select" label="Keep" name="orientation"> - <option value="most-intense">Most intense peaks</option> - <option value="least-intense">Least intense peaks</option> - </param> - </repeat> - - <conditional name="filter_mz_windows"> - <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> - <when value="false" /> - <when value="true"> - <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" /> - <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" /> - </when> - </conditional> - - <conditional name="etd_filtering"> - <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" /> - <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> - <option value="MZ" selected="true">mz</option> - <option value="PPM">ppm</option> - </param> - </when> - </conditional> - - <conditional name="ms2denoise"> - <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" /> - <when value="true"> - <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" /> - <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" /> - <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" /> - </when> - <when value="false" /> - </conditional> - - <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> - - </section> - - - <section name="filtering" title="Scan Inclusion/Exclusion Filters"> - - <param name="activation" type="select" label="Filter by Activation"> - <option value="false" selected="true">no</option> - <option value="ETD">ETD</option> - <option value="CID">CID</option> - <option value="SA">SA</option> - <option value="HCD">HCD</option> - <option value="BIRD">BIRD</option> - <option value="ECD">ECD</option> - <option value="IRMPD">IRMPD</option> - <option value="PD">PD</option> - <option value="PSD">PSD</option> - <option value="PQD">PQD</option> - <option value="SID">SID</option> - <option value="SORI">SORI</option> - </param> - - <repeat name="indices" title="Filter Scan Indices"> - <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> - </repeat> - - <repeat name="scan_numbers" title="Filter Scan Numbers"> - <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> - </repeat> - - <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> - - <conditional name="filter_ms_levels"> - <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" /> - <when value="false" /> - <when value="true"> - <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" /> - <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" /> - </when> - </conditional> - - <param name="polarity" type="select" label="Filter by Polarity"> - <option value="false" selected="true">no</option> - <option value="positive">positive</option> - <option value="negative">negative</option> - </param> - - <param name="analyzer" type="select" label="Filter by Analyzer"> - <option value="false" selected="true">no</option> - <option value="quad">Quadrupole</option> - <option value="orbi">Orbitrap</option> - <option value="FT">Fourier-transform</option> - <option value="IT">Ion trap</option> - <option value="TOF">Time of flight</option> - </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"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="intensity_encoding" label="Intensity Encoding Precision"> - <option value="64">64</option> - <option value="32" selected="true">32</option> - </param> - <param type="select" name="binary_compression" label="Binary data compression"> - <option value="false">None</option> - <option value="zlib" selected="true">zlib</option> - <option value="numpressLinearPic">numpressLinear/numpressPic</option> - <option value="numpressLinearSlof">numpressLinear/numpressSlof</option> - <option value="numpressLinear">numpressLinear only</option> - <option value="numpressPic">numpressPic only</option> - <option value="numpressSlof">numpressSlof only</option> - </param> - <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" /> - </section> - </xml> - - <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> - <change_format> - <when input="output_type" value="mz5" format="mz5" /> - <when input="output_type" value="mzxml" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - <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> - - - <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" 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" /> -<<<<<<< HEAD - <param name="output_type" value="mzml" /> - <output name="output" file="MassLynxTest.mzML" /> -======= - <param name="output_type" value="mzML" /> - <output name="output" file="MassLynxTest.mzML" lines_diff="4" /> ->>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213 - </test> - <test> - <param name="input" value="AgilentMassHunterTest.d.tar" /> - <param name="license_agreement" value="true" /> -<<<<<<< HEAD - <param name="output_type" value="mzxml" /> - <output name="output" file="AgilentMassHunterTest.mzXML" /> -======= - <param name="output_type" value="mzXML" /> - <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" /> ->>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213 - </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" lines_diff="6" /> - </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="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" 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="gzip_compression" value="true" /> - <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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="gzip_compression" value="true" /> - <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="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="binary_compression" value="numpressLinearPic" /> - <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" 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" 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" 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" 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" /> - <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" /> - </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" /> - <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" 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" /> - <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" 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" /> - <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" /> - </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" /> - <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" /> - </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" 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" 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" 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" 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" /> - <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" /> - </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" 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" 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" 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" 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" /> - <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"/> <!-- the scan numbers here produce the same output as the index test above --> - </test> - <!--<test> - <param name="input" value="small.mzML" /> - <param name="output_type" value="mzml" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-deisotope-poisson.mzML" /> - </test>--> - </xml> - <xml name="msconvert_help"> -**What it does** - -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_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - </xml> - - <xml name="citations"> - <citations> - <citation type="doi">10.1093/bioinformatics/btn323</citation> - <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, - year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> - </citations> - </xml> - -</macros>