msconvert: msconvert_macros.xml comparison

comparison msconvert_macros.xml @ 7:e638f7fad66a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292

author	galaxyp
date	Sat, 23 Feb 2019 06:21:27 -0500
parents	6b6bba73eadb
children	dff86cbe69f2

comparison

equal deleted inserted replaced

-:6b6bba73eadb
+:e638f7fad66a
 <macros>
-<xml name="generic_requirements">
+<token name="@VERSION@">3.0.19052</token>
-<requirements>
+<token name="@FULL_VERSION@">@VERSION@-089e81090</token>
-<requirement type="package" version="3.0.9992">proteowizard</requirement>
-</requirements>
-</xml>
-<token name="@VERSION@">3.0.9992</token>
 <xml name="msconvertCommand">
-<command interpreter="python">
+<command detect_errors="exit_code">
 <![CDATA[
 #import re
 #set $ext = $input.ext
 ## sanitize display name for use as temp filename
-#set basename = 'pwiz_in'
+#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 hasattr($input, 'display_name')
+#if $data_processing.precursor_refinement.use_mzrefinement
-## explicit inclusion or exclusion ??
+#set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
-#set basename = $re.sub(r'[^\w\.\-\+]','_',$input.display_name)
+#set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
-##set basename = $re.sub(r'[\/\\\;\|\&\>\<]','_',$input.display_name)
+ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
 #end if
-msconvert_wrapper.py
+uid=`id -u` &&
+gid=`id -g` &&
-#if $ext == 'wiff':
---input='${input.extra_files_path}/wiff'
+wine64_anyuser msconvert '${basename}'
---input_name='${basename}.wiff'
+--outdir outputs
---implicit='${input.extra_files_path}/wiff_scan'
+--${output_type}
---input='${input.extra_files_path}/wiff_scan'
---input_name='${basename}.wiff.scan'
+#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},${index.to}]
+#end for
+"
+#end if
 #else
---input='${input}'
+--runIndexSet $general_options.multi_run_output.runIndexSet
---input_name='$basename'
 #end if
---output='${output}'
-## BEGIN_VERSION_DEFAULT
+## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests
---fromextension=$ext
+--stripLocationFromSourceFiles
-## END_VERSION_DEFAULT
---toextension=${output_type}
 ## 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 $data_processing.precursor_refinement.use_mzrefinement
-#set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext))
---ident='$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"
+maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"
-#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"
 #end if
 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
 --filter "chargeStatePredictor
 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
 #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 $data_processing.etd_filtering.matching_tolerance_units"
+$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 $data_processing.ms2denoise.relax"
 #end if
 #if str($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
 #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' -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>
 <option value="mzXML">mzXML</option>
 <option value="mgf">mgf</option>
 <option value="ms2">ms2</option>
 </param>
 <section name="data_processing" title="Data Processing Filters">
+<conditional name="peak_picking">
-<conditional name="peak_picking">
+<param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
-<param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
+<when value="false" />
-<when value="false" />
+<when value="true">
-<when value="true">
+<param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
-<param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
+<option value="1">MS1 Only (1)</option>
-<option value="1">MS1 Only (1)</option>
+<option value="2">MS2 Only (2)</option>
-<option value="2">MS2 Only (2)</option>
+<option value="2-">MS2 and on (2-)</option>
-<option value="2-">MS2 and on (2-)</option>
+<option value="1-" selected="true">All Levels (1-)</option>
-<option value="1-" selected="true">All Levels (1-)</option>
+</param>
-</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)">
-<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="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
+<option value="cwt">CantWaiT - continuous wavelet transform</option>
-<option value="cwt">CantWaiT - continuous wavelet transform</option>
+</param>
-</param>
+</when>
-</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>
 <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>
 </section>
 </xml>
 <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" />
 <when input="output_type" value="ms2" format="ms2" />
 <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>
 <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="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>
 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
 <param name="output_type" value="mzXML" />
 <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="output_type" value="mzML" />
+<param name="license_agreement" value="true" />
-<param name="binary_compression" value="numpressLinearPic" />
+<param name="output_type" value="mzML" />
-<output name="output" file="small-numpressLP.mzML" />
+<param name="binary_compression" value="numpressLinearPic" />
-</test>
+<output name="output" file="small-numpressLP.mzML" lines_diff="114" />
+</test>
-<test>
-<param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+<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" />
 <param name="thresholdScore" value="mvh" />
 <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" />
+<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" />
+<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="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" />
+<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" />
 <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" />
+<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" />
 <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" /> <!-- 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" />
 <param name="output_type" value="mzML" />
 <param name="binary_compression" value="numpressLinearPic" />
 </test>-->
 </xml>
 <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_.
 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
 </xml>

Mercurial > repos > galaxyp > msconvert

comparison msconvert_macros.xml @ 7:e638f7fad66a draft