Mercurial > repos > galaxyp > msconvert
diff msconvert.xml @ 6:6b6bba73eadb draft
planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
author | galaxyp |
---|---|
date | Tue, 14 Mar 2017 16:52:39 -0400 |
parents | 637e309295cf |
children | e638f7fad66a |
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--- a/msconvert.xml Mon Dec 12 17:07:11 2016 -0500 +++ b/msconvert.xml Tue Mar 14 16:52:39 2017 -0400 @@ -1,269 +1,378 @@ <tool id="msconvert" name="msconvert" version="0.3.0"> - <description>Convert and/or filter mass spectrometry files</description> + <!-- BEGIN_VERSION_DEFAULT --> + <description>Convert and filter a mass spec peak list</description> + <!-- END_VERSION_DEFAULT --> + <!-- + <requirements> + <requirement type="package" version="3_0_4388">proteowizard</requirement> + </requirements> +--> + <command interpreter="python"> + #import re + #set $ext = $input.ext + msconvert_wrapper.py + #if $type.input_type == 'wiff': + #set basename = 'absciex' + #if hasattr($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 - <macros> - <import>msconvert_macros.xml</import> - </macros> + + --toextension=${output_type} - <requirements> - <requirement type="package" version="3.0.9992">proteowizard</requirement> - </requirements> + #if $settings.settingsType == "full" + --binaryencoding=${settings.binary_encoding} + --mzencoding=${settings.mz_encoding} + --intensityencoding=${settings.intensity_encoding} + --zlib=${settings.zlib} + #end if - <expand macro="msconvertCommand" /> + #if $filtering.filtering_use - <inputs> - <param format="mzml,mzxml,mz5,mgf,ms2" name="input" type="data" label="Input unrefined MS data" /> + #if $filtering.precursor_recalculation.value + --filter "precursorRecalculation" + #end if + + #if $filtering.peak_picking.pick_peaks + --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" + #end if - <expand macro="msconvertInputParameters" /> - </inputs> + #if str($filtering.activation) != "false" + --filter "activation $filtering.activation" + #end if - <expand macro="msconvertOutput" /> + #if len($filtering.indices) > 0 + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " + #end if - <tests> - <test> - <param name="input" value="small.mzML" /> - <param name="output_type" value="mzML" /> - <param name="pick_peaks" value="true" /> - <param name="pick_peaks_algorithm" value="cwt" /> - <param name="pick_peaks_ms_levels" value="1-" /> - <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> - </test> + #if len($filtering.scan_numbers) > 0 + --filter "scanNumber + #for $scan_number in $filtering.scan_numbers + [${scan_number.from},${scan_number.to}] + #end for + " + #end if + + #for threshold_entry in $filtering.threshold_repeat + --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation" + #end for + + + #if $filtering.strip_it.value + --filter "stripIT" + #end if + + #if $filtering.filter_mz_windows.do_filter + --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" + #end if + + + #if $filtering.filter_ms_levels.do_filter + --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" + #end if - <!-- this data file only has profile MS1, so the result is the same --> - <test> - <param name="input" value="small.mzML" /> - <param name="output_type" value="mzML" /> - <param name="pick_peaks" value="true" /> - <param name="pick_peaks_algorithm" value="cwt" /> - <param name="pick_peaks_ms_levels" value="1" /> - <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mz5" /> - <param name="mz_encoding" value="64" /> - <param name="intensity_encoding" value="64" /> - <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzXML" /> - <param name="mz_encoding" value="32" /> - <param name="intensity_encoding" value="32" /> - <output name="output" file="small-zlib-32.mzXML" /> - </test> - <!-- TODO: how to test gzipped output? - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzXML" /> - <param name="mz_encoding" value="32" /> - <param name="intensity_encoding" value="32" /> - <param name="binary_compression" value="false" /> - <param name="gzip_compression" value="true" /> - <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" /> - </test> - <test> - <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> - <param name="output_type" value="mzML" /> - <param name="mz_encoding" value="32" /> - <param name="intensity_encoding" value="32" /> - <param name="binary_compression" value="false" /> - <param name="gzip_compression" value="true" /> - <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" /> - </test>--> + #if str($filtering.etd_filtering.do_etd_filtering) == "default" + --filter "ETDFilter" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" + --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" + #end if + + ## BEGIN_VERSION_3 + + #if $filtering.precursor_refine.value + --filter "precursorRefine" + #end if + + #if $filtering.ms2denoise.denoise + --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax" + #end if + + #if str($filtering.ms2deisotope) == "true" + --filter "MS2Deisotope" + #end if + + #if str($filtering.polarity) != "false" + --filter "polarity $filtering.polarity" + #end if + + #if str($filtering.analyzer) != "false" + --filter "analyzer $filtering.analyzer" + #end if + + ## END_VERSION_3 + + #end if + + </command> + + <inputs> - <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> + <!-- BEGIN_VERSION_DEFAULT --> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="mzml">mzML</option> + <option value="mzxml">mzXML</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + <option value="wiff">wiff</option> + </param> + <when value="mzml"> + <param format="mzml" name="input" type="data" label="Input mzML"/> + </when> + <when value="mzxml"> + <param format="mzxml" name="input" type="data" label="Input mzXML"/> + </when> + <when value="mgf"> + <param format="mgf" name="input" type="data" label="Input mgf"/> + </when> + <when value="ms2"> + <param format="ms2" name="input" type="data" label="Input ms2"/> + </when> + <when value="wiff"> + <param format="wiff" name="input" type="data" label="Input wiff"/> + </when> + </conditional> + <!-- END_VERSION_DEFAULT --> + <param name="output_type" type="select" label="Output Type"> + <option value="mzML">mzML (indexed)</option> + <option value="unindexed_mzML">mzML (unindexed)</option> + <option value="mzXML">mzXML (indexed)</option> + <option value="unindexed_mzXML">mzXML (unindexed)</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <conditional name="filtering"> + <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> + <!-- BEGIN_VERSION_3 --> + <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> + <!-- END_VERSION_3 --> - <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> + <conditional name="peak_picking"> + <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="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-">All Levels (1-)</option> + </param> + <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> + </when> + </conditional> - <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>--> - </tests> + <repeat name="threshold_repeat" title="Filter by Threshold"> + <conditional name="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><!-- TODO: absolute what? m/z --> + <option value="bpi-relative">Percent of base peak intensity</option> + <option value="tic-relative">Percent of total ion current</option> + <option value="tic-fraction">Aggregate percent of total ion current</option> + </param> + <when value="count"> + <param type="integer" name="value" label="Number of peaks to keep" value="100" /> + </when> + <when value="count-after-ties"> + <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> + </when> + <when value="absolute"> + <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> + </when> + <when value="bpi-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" + /> + </when> + <when value="tic-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" + /> + </when> + <when value="tic-fraction"> + <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> + </when> + </conditional> + <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> + + + <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> + <!-- BEGIN_VERSION_3 --> + <option>BIRD</option> + <option>ECD</option> + <option>IRMPD</option> + <option>PD</option> + <option>PSD</option> + <option>PQD</option> + <option>SID</option> + <option>SORI</option> + <!-- END_VERSION_3 --> + </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> + + <conditional name="filter_mz_windows"> + <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> + <when value="false" /> + <when value="true"> + <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> + <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> + </when> + </conditional> + + <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> + + <conditional name="filter_ms_levels"> + <param name="do_filter" type="boolean" label="Filter MS Levels" /> + <when value="false" /> + <when value="true"> + <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> + </when> + </conditional> + + <conditional name="etd_filtering"> + <param name="do_etd_filtering" type="select" label="ETD Filtering"> + <option value="none" selected="true">none</option> + <option value="default">yes (with default options)</option> + <option value="advanced">yes (show advanced options) </option> + </param> + <when value="none" /> + <when value="default" /> + <when value="advanced"> + <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> + </param> + <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> + <param name="remove_precursor" type="select" label="ETD Remove 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"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="blanket_removal" type="select" label="ETD Blanket Removal"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + </when> + </conditional> + + + <!-- BEGIN_VERSION_3 --> + <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" /> + + <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">quad</option> + <option value="orbi">orbi</option> + <option value="FT">FT</option> + <option value="IT">IT</option> + <option value="TOF">TOF</option> + </param> + <!-- END_VERSION_3 --> + </when> + </conditional> + + <conditional name="settings"> + <param name="settingsType" type="select" label="Advanced Settings" help=""> + <option value="default">Use Defaults</option> + <option value="full">Full Parameter List</option> + </param> + <when value="default" /> + <when value="full"> + <param type="select" name="binary_encoding" label="Binary Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <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" value="32"> + <option value="64">64</option> + <option value="32" selected="true">32</option> + </param> + <param type="boolean" name="zlib" label="Use zlib"> + </param> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" > + <change_format> + <when input="output_type" value="mzXML" format="mzxml" /> + <when input="output_type" value="unindexed_mzXML" format="mzxml" /> + <when input="output_type" value="ms2" format="ms2" /> + <when input="output_type" value="mgf" format="mgf" /> + </change_format> + </data> + </outputs> <help> **What it does** @@ -272,10 +381,15 @@ You can view the original documentation here_. .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html + +------ + +**Citation** + +For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` + +If you use this tool in Galaxy, please cite Chilton J, et al. +https://github.com/galaxyproteomics/tools-galaxyp/ + </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btn323</citation> - <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, - year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> - </citations> </tool>