Mercurial > repos > galaxyp > idconvert
changeset 2:edb33e8224c6 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
| author | galaxyp |
|---|---|
| date | Sat, 23 Feb 2019 06:21:11 -0500 |
| parents | 9e6e840d6b52 |
| children | |
| files | idconvert.xml msconvert_macros.xml tool_dependencies.xml |
| diffstat | 3 files changed, 45 insertions(+), 725 deletions(-) [+] |
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--- a/idconvert.xml Mon Aug 08 10:43:52 2016 -0400 +++ b/idconvert.xml Sat Feb 23 06:21:11 2019 -0500 @@ -1,9 +1,8 @@ <tool id="idconvert" name="idconvert" version="@VERSION@.0"> <description>Convert mass spectrometry identification files</description> - <macros> - <import>msconvert_macros.xml</import> - </macros> - <expand macro="generic_requirements" /> + <requirements> + <requirement type="package" version="3.0.9992">proteowizard</requirement> + </requirements> <stdio> <exit_code range="1:" /> <regex match="Error" @@ -15,15 +14,15 @@ <![CDATA[ #import os.path #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')]) -ln -s "$from.input" "$input_name" && -idconvert $input_name +ln -s '$from.input' '$input_name' && +idconvert '$input_name' #if str($to_format) == 'pep.xml': --pepXML #elif str($to_format) == 'text': --text #end if ---outdir outdir -&& cp outdir/* $output +--outdir 'outdir' +&& cp outdir/* '$output' ]]> </command> <inputs> @@ -49,40 +48,40 @@ <option value="pep.xml">pepXML (pepxml)</option> <option value="text">text</option> </param> - </inputs> - <outputs> - <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}"> - <change_format> - <when input="to_format" value="pep.xml" format="pepxml" /> - <when input="to_format" value="text" format="txt" /> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="input" value="Rpal_01.pepXML" /> - <param name="from_format" value="pepxml" /> - <param name="to_format" value="mzid" /> - <output name="output_psms"> - <assert_contents> - <has_text text="MzIdentML" /> - <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> - </assert_contents> - </output> - </test> - <test> - <param name="input" value="Rpal_01.mzid" /> - <param name="from_format" value="mzid" /> - <param name="to_format" value="pep.xml" /> - <output name="output_psms"> - <assert_contents> - <has_text text="msms_pipeline_analysis" /> - <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> - </assert_contents> - </output> - </test> - </tests> - <help> + </inputs> + <outputs> + <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}"> + <change_format> + <when input="to_format" value="pep.xml" format="pepxml" /> + <when input="to_format" value="text" format="txt" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input" value="Rpal_01.pepXML" /> + <param name="from_format" value="pepxml" /> + <param name="to_format" value="mzid" /> + <output name="output"> + <assert_contents> + <has_text text="MzIdentML" /> + <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="Rpal_01.mzid" /> + <param name="from_format" value="mzid" /> + <param name="to_format" value="pep.xml" /> + <output name="output"> + <assert_contents> + <has_text text="msms_pipeline_analysis" /> + <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> + </assert_contents> + </output> + </test> + </tests> + <help> <![CDATA[ idconvert [options] [filemasks] Convert mass spec identification file formats. @@ -118,6 +117,8 @@ idconvert mascot.mzid --pepXML ]]> - </help> - <expand macro="citations" /> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btn323</citation> + </citations> </tool>
--- a/msconvert_macros.xml Mon Aug 08 10:43:52 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,675 +0,0 @@ -<macros> - <xml name="generic_requirements"> - <requirements> - <requirement type="package" version="3.0.9016">proteowizard</requirement> - </requirements> - </xml> - <token name="@VERSION@">3.0</token> - - <xml name="msconvertCommand"> - <command interpreter="python"> -<![CDATA[ - #import re - #set $ext = $input.ext - msconvert_wrapper.py - #if $ext == 'wiff': - #set basename = 'absciex' - #if hasattr($input, 'display_name') - #set basename = $re.sub('\W','_',$input.display_name) - #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 - #end if - --output=${output} - ## BEGIN_VERSION_DEFAULT - --fromextension=$ext - ## 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.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" - #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 - -]]> - </command> - </xml> - - <xml name="msconvertInputParameters"> - <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"> - <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" title="MZRefinery Precursor Refinement" expanded="true"> - <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+" /> - <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="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>BIRD</option> - <option>ECD</option> - <option>IRMPD</option> - <option>PD</option> - <option>PSD</option> - <option>PQD</option> - <option>SID</option> - <option>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="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.rsplit('.',1)[0]}.${output_type}" > - <change_format> - <when input="output_type" value="mz5" format="mz5" /> - <when input="output_type" value="mzXML" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv"> - <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter> - </data> - </outputs> - </xml> - - - <xml name="msconvert_tests"> - <test> - <param name="input" value="small.mzML" /> - <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" /> - </test> - - <!-- this data file only has profile MS1, so the result is the same --> - <test> - <param name="input" value="small.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <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" /> - <output name="output" file="small-zlib-32.mzXML" /> - </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="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-numpressLP.mzML" /> - </test> - - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinearSlof" /> - <output name="output" file="small-numpressLS.mzML" /> - </test> - - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressLinear" /> - <output name="output" file="small-numpressL.mzML" /> - </test> - - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressPic" /> - <output name="output" file="small-numpressP.mzML" /> - </test> - - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzML" /> - <param name="binary_compression" value="numpressSlof" /> - <output name="output" file="small-numpressS.mzML" /> - </test> - - <test> - <param name="input" value="Rpal_01.mz5" /> - <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="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="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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" /> - <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="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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzML" /> - <param name="ms2deisotope" value="true" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-deisotope.mzML" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzML" /> - <param name="activation" value="CID" /> - <param name="binary_compression" value="numpressLinearPic" /> - <output name="output" file="small-activation.mzML" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <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 --> - </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** - -Allows interconversion within various mass spectrometry peak list 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>
--- a/tool_dependencies.xml Mon Aug 08 10:43:52 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="proteowizard" version="3.0.9016"> - <repository changeset_revision="e9ae8f0be737" name="package_proteowizard_3_0_9016" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>