Mercurial > repos > jjohnson > spectrast
diff spectrast_search.xml @ 1:390a3c4a7f6b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty
| author | jjohnson |
|---|---|
| date | Mon, 18 Jun 2018 10:08:02 -0400 |
| parents | |
| children | e67b0cc10377 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spectrast_search.xml Mon Jun 18 10:08:02 2018 -0400 @@ -0,0 +1,426 @@ +<tool id="specrast_search" name="SpectraST Search" version="@VERSION@.0"> + <description>with Spectral Library</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + ## Need to symlink to data using name with extension that spectrast recognizes + #import re + ## spectrum datasets + #set $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'msp': 'msp', 'mzdata':'mzData'} + #set $input_files = [] + #def ln_scan($sf): + #set $ext = $exts[$sf.extension.lower()] + #set $input_name = $re.sub('[.]([^.]*)$','$ext',$sf.display_name.split('/')[-1]) + #silent $input_files.append($input_name) + ln -s -f '${sf}' '${input_name}' && + #set $encoded_id = $__app__.security.encode_id($sf.id) + echo "Spectrums:${sf.display_name}(API:${encoded_id}) "; + #end def + #if $collection.collection_selector == 'dataset': + ln_scan($collection.spectrum_file) + #else: + #for $spectrum_file in $spectrum_files: + ln_scan($collection.spectrum_file) + #end for + #end if + python $__tool_directory__/spectrast_params.py + #if def $spectrastParams: + '$spectrastParams' + #end if + $spectrast_params' -o spectrast.params && + mkdir out && + spectrast -sFspectrast.params -sL'${libraryFile.files_path}/library.splib' -sE $output_format + #echo ' '.join($input_files) + #if $collection.collection_selector == 'dataset': + && cp out/* $output + #end if + ]]></command> + <configfiles> + <configfile name="spectrast_params"><![CDATA[#slurp +libraryFile = $libraryFile +#if $databaseFile is not None: +databaseFile = $databaseFile +#end if +#if $databaseType is not None: +databaseType = $databaseType +#end if +#if $indexCacheAll is not None: +indexCacheAll = $indexCacheAll +#end if +#if $filterSelectedListFileName is not None: +filterSelectedListFileName = $filterSelectedListFileName +#end if +#if $candidate_selection_and_scoring.precursorMzTolerance is not None: +precursorMzTolerance = $candidate_selection_and_scoring.precursorMzTolerance +#end if +#if $candidate_selection_and_scoring.precursorMzUseAverage is not None: +precursorMzUseAverage = $candidate_selection_and_scoring.precursorMzUseAverage +#end if +#if $candidate_selection_and_scoring.searchAllCharges is not None: +searchAllCharges = $candidate_selection_and_scoring.searchAllCharges +#end if +#if $candidate_selection_and_scoring.detectHomologs is not None: +detectHomologs = $candidate_selection_and_scoring.detectHomologs +#end if +#if $candidate_selection_and_scoring.fvalFractionDelta is not None: +fvalFractionDelta = $candidate_selection_and_scoring.fvalFractionDelta +#end if +#if $candidate_selection_and_scoring.useSp4Scoring is not None: +useSp4Scoring = $candidate_selection_and_scoring.useSp4Scoring +#end if +#if $candidate_selection_and_scoring.fvalUseDotBias is not None: +fvalUseDotBias = $candidate_selection_and_scoring.fvalUseDotBias +#end if +#if $candidate_selection_and_scoring.usePValue is not None: +usePValue = $candidate_selection_and_scoring.usePValue +#end if +#if $candidate_selection_and_scoring.useTierwiseOpenModSearch is not None: +useTierwiseOpenModSearch = $candidate_selection_and_scoring.useTierwiseOpenModSearch +#end if +#if $outputExtension is not None: +outputExtension = $outputExtension +#end if +#if $outputDirectory is not None: +outputDirectory = $outputDirectory +#end if +#if $output_and_display.hitListTopHitFvalThreshold is not None: +hitListTopHitFvalThreshold = $output_and_display.hitListTopHitFvalThreshold +#end if +#if $output_and_display.hitListLowerHitsFvalThreshold is not None: +hitListLowerHitsFvalThreshold = $output_and_display.hitListLowerHitsFvalThreshold +#end if +#if $output_and_display.hitListShowHomologs is not None: +hitListShowHomologs = $output_and_display.hitListShowHomologs +#end if +#if $output_and_display.hitListShowMaxRank is not None: +hitListShowMaxRank = $output_and_display.hitListShowMaxRank +#end if +#if $output_and_display.hitListOnlyTopHit is not None: +hitListOnlyTopHit = $output_and_display.hitListOnlyTopHit +#end if +#if $output_and_display.hitListExcludeNoMatch is not None: +hitListExcludeNoMatch = $output_and_display.hitListExcludeNoMatch +#end if +#if $output_and_display.enzymeForPepXMLOutput is not None: +enzymeForPepXMLOutput = $output_and_display.enzymeForPepXMLOutput +#end if +#if $printFingerprintingSummary is not None: +printFingerprintingSummary = $printFingerprintingSummary +#end if +#if $spectrum_filtering.filterMinPeakCount is not None: +filterMinPeakCount = $spectrum_filtering.filterMinPeakCount +#end if +#if $spectrum_filtering.filterAllPeaksBelowMz is not None: +filterAllPeaksBelowMz = $spectrum_filtering.filterAllPeaksBelowMz +#end if +#if $spectrum_filtering.filterMaxIntensityBelow is not None: +filterMaxIntensityBelow = $spectrum_filtering.filterMaxIntensityBelow +#end if +#if $spectrum_filtering.filterMinMzRange is not None: +filterMinMzRange = $spectrum_filtering.filterMinMzRange +#end if +#if $spectrum_filtering.filterCountPeakIntensityThreshold is not None: +filterCountPeakIntensityThreshold = $spectrum_filtering.filterCountPeakIntensityThreshold +#end if +#if $spectrum_processing.filterRemovePeakIntensityThreshold is not None: +filterRemovePeakIntensityThreshold = $spectrum_processing.filterRemovePeakIntensityThreshold +#end if +#if $spectrum_processing.filterMaxPeaksUsed is not None: +filterMaxPeaksUsed = $spectrum_processing.filterMaxPeaksUsed +#end if +#if $spectrum_processing.filterMaxDynamicRange is not None: +filterMaxDynamicRange = $spectrum_processing.filterMaxDynamicRange +#end if +#if $spectrum_processing.peakScalingMzPower is not None: +peakScalingMzPower = $spectrum_processing.peakScalingMzPower +#end if +#if $spectrum_processing.peakScalingIntensityPower is not None: +peakScalingIntensityPower = $spectrum_processing.peakScalingIntensityPower +#end if +#if $spectrum_processing.peakScalingUnassignedPeaks is not None: +peakScalingUnassignedPeaks = $spectrum_processing.peakScalingUnassignedPeaks +#end if +#if $spectrum_processing.peakNoBinning is not None: +peakNoBinning = $spectrum_processing.peakNoBinning +#end if +#if $spectrum_processing.peakBinningNumBinsPerMzUnit is not None: +peakBinningNumBinsPerMzUnit = $spectrum_processing.peakBinningNumBinsPerMzUnit +#end if +#if $spectrum_processing.peakBinningFractionToNeighbor is not None: +peakBinningFractionToNeighbor = $spectrum_processing.peakBinningFractionToNeighbor +#end if +#if $spectrum_processing.filterLibMaxPeaksUsed is not None: +filterLibMaxPeaksUsed = $spectrum_processing.filterLibMaxPeaksUsed +#end if +#if $spectrum_processing.filterLightIonsMzThreshold is not None: +filterLightIonsMzThreshold = $spectrum_processing.filterLightIonsMzThreshold +#end if +#if $spectrum_processing.filterITRAQReporterPeaks is not None: +filterITRAQReporterPeaks = $spectrum_processing.filterITRAQReporterPeaks +#end if +#if $spectrum_processing.filterTMTReporterPeaks is not None: +filterTMTReporterPeaks = $spectrum_processing.filterTMTReporterPeaks +#end if +]]> + </configfile> + </configfiles> + <inputs> + <conditional name="collection"> + <param name="collection_selector" type="select" label="Process Spectrums Indivdiual or Collection "> + <option value="dataset" selected="true">Search Single Spectrum file and output results as a dataset</option> + <option value="collection">Search Multiple Spectrum files and output results as a collection</option> + </param> + <when value="dataset"> + <param name="spectrum_file" type="data" format="mzxml,mzml,mgf,msp,mzdata" label="Spectrum file" help="mzxml,mzml,mgf,msp,mzdata"/> + </when> + <when value="collection"> + <param name="spectrum_files" multiple="true" type="data" format="mzxml,mzml,mgf,msp,mzdata" label="Spectrum files" help="mzxml,mzml,mgf,msp,mzdata"/> + </when> + </conditional> + + <param name="libraryFile" type="data" format="splib" label="Spectral library" help=""/> + <param name="spectrastParams" type="data" format="txt" optional="true" label="SpectraST param file" help=""/> + <section name="general" expanded="false" title="General Options"> + <param name="databaseFile" type="data" format="fasta" label="Fasta sequence database" optional="true" + help="will not affect the search in any way, but this information will be included in the output for any downstream data processing."/> + <param name="databaseType" type="select" label="Database type: Protein or DNA" > + <option value="AA" selected="true">protein AA</option> + <option value="DNA">genomic DNA</option> + </param> + <param name="indexCacheAll" type="boolean" label="indexCacheAll" help="Cache all entries in RAM. Requires a lot of memory (the library will usually be loaded almost in its entirety), but speeds up search for unsorted queries."/> + </section> + <section name="candidate_selection_and_scoring" expanded="false" title="Candidate Selection and Scoring Options"> + <param name="precursorMzTolerance" type="float" value="" optional="true" + label="precursorMzTolerance" + help="Specify precursor m/z tolerance in Th. Monoisotopic mass is assumed. Default is 3.0"/> + <param name="precursorMzUseAverage" type="select" optional="true" label="precursorMzUseAverage Default: false" > + <help> Report average mass instead of monoisotopic mass in search results. + Precursor m/z window is expanded to account for difference between average and monoisotopic mass. + </help> + <option value="false">false</option> + <option value="true">true</option> + </param> + <param name="searchAllCharges" type="select" optional="true" label="searchAllCharges Default: false" > + <help> Report average mass instead of monoisotopic mass in search results. + Precursor m/z window is expanded to account for difference between average and monoisotopic mass. + </help> + <option value="false">false</option> + <option value="true">true</option> + </param> + <param name="detectHomologs" type="integer" value="" optional="true" + label="detectHomologs" + help="Detect homologous lower hits up to this rank. Looks for lower hits homologous to the top hit and adjust delta accordingly. Default is 4"/> + <param name="fvalFractionDelta" type="float" value="" optional="true" + label="fvalFractionDelta" + help="Specify the fraction of the normalized delta score (delta/dot) in the F-value formula. Default is 0.4"/> + <param name="useSp4Scoring" type="select" optional="true" label="useSp4Scoring (SP4) Default: false" > + <help> Use original SpectraST (4.0 or earlier) scoring, based on dot products of square-root intensities. + </help> + <option value="false">false</option> + <option value="true">true</option> + </param> + <param name="fvalUseDotBias" type="select" optional="true" label="fvalUseDotBias (Only applicable for SP4 scoring) Default: true" > + <help> Use dot bias to penalize high-scoring matches with massive noise and/or dominant peak. + </help> + <option value="true">true</option> + <option value="false">false</option> + </param> + <param name="usePValue" type="select" optional="true" label="usePValue (NOT applicable for SP4 scoring) Default: false" > + <help> Use dot bias to penalize high-scoring matches with massive noise and/or dominant peak. + </help> + <option value="false">false</option> + <option value="true">true</option> + </param> + <param name="useTierwiseOpenModSearch" type="select" optional="true" label="useTierwiseOpenModSearch (NOT applicable for SP4 scoring) Default: false" > + <help> Perform tier-wise open modification search for modifications within precursor m/z window specified. + Note that the scoring is different from normal SpectraST searches. + </help> + <option value="false">false</option> + <option value="true">true</option> + </param> + </section> + <section name="output_and_display" expanded="false" title="Output and Display Options"> + <param name="hitListTopHitFvalThreshold" type="float" value="" optional="true" + label="hitListTopHitFvalThreshold" + help="Minimum F value threshold for the top hit. Only top hits having F value greater than this will be printed. Default is 0.0 (all top hits)"/> + <param name="hitListLowerHitsFvalThreshold" type="float" value="" optional="true" + label="hitListLowerHitsFvalThreshold" + help="Minimum F value threshold for the lower hits. Only lower hits having F value greater than this will be printed. Default=0.45"/> + <param name="hitListShowHomologs" type="select" optional="true" label="hitListShowHomologs Default: true" > + <help> Always displays homologous lower hits regardless of F value. + </help> + <option value="true">true</option> + <option value="false">false</option> + </param> + <param name="hitListShowMaxRank" type="integer" value="" optional="true" min="1" + label="hitListShowMaxRank" + help="Maximum rank for hits shown for each query. Default is 1 (Just the top hit)"/> + <param name="hitListOnlyTopHit" type="select" optional="true" label="hitListOnlyTopHit Default: true" > + <help> Only display the top hit for each query. + </help> + <option value="true">true</option> + <option value="false">false</option> + </param> + <param name="hitListExcludeNoMatch" type="select" optional="true" label="hitListExcludeNoMatch Default: true" > + <help> Do not display queries for which there is no candidate, or the top hit is below the minimum F value threshold specified. + </help> + <option value="true">true</option> + <option value="false">false</option> + </param> + <param name="enzymeForPepXMLOutput" type="text" value="trypsin" optional="true" label="enzymeForPepXMLOutput"> + <help>Specify the proteolytic enzyme used, for the purpose of pepXML output. + </help> + <option value="trypsin">trypsin</option> + <option value="lysc">lysc</option> + </param> + </section> + <section name="spectrum_filtering" expanded="false" title="Spectrum Filtering Options"> + <param name="filterMinPeakCount" type="integer" value="" optional="true" min="1" + label="filterMinPeakCount" + help="Discard query spectra with fewer than peaks above set threshold. Default is 10"/> + <param name="filterAllPeaksBelowMz" type="integer" value="" optional="true" min="1" + label="filterAllPeaksBelowMz" + help="Discard query spectra with almost no peaks above specified m/z value. All query spectra with 95%+ of the total intensity below m/z will be removed. Default is 520"/> + <param name="filterMaxIntensityBelow" type="integer" value="" optional="true" min="0" + label="filterMinPeakCount" + help="Discard query spectra with no peaks with intensity above this. Default is 0"/> + <param name="filterMinMzRange" type="integer" value="" optional="true" min="0" + label="filterMinMzRange" + help="Discard query spectra with m/z range narrower than this. Default 350"/> + <param name="filterCountPeakIntensityThreshold" type="float" value="" optional="true" + label="filterCountPeakIntensityThreshold" + help="Minimum peak intensity for peaks to be counted. Only peaks with intensity above this will be counted to meet the requirement for minimum number of peaks. Default is 2.01"/> + </section> + <section name="spectrum_processing" expanded="false" title="Spectrum Processing Options"> + <param name="filterRemovePeakIntensityThreshold" type="float" value="" optional="true" + label="filterRemovePeakIntensityThreshold" + help="Noise peak threshold. All peaks with intensities below this will be zeroed. Default is 2.01"/> + <param name="filterMaxPeaksUsed" type="integer" value="" optional="true" min="1" + label="filterMaxPeaksUsed" + help="Remove all but the top number peaks in query spectra. Default 150"/> + <param name="filterMaxDynamicRange" type="integer" value="" optional="true" min="1" + label="filterMaxDynamicRange" + help="Remove all peaks smaller than 1/number of the base (highest) peak in query spectra. Default 1000"/> + + <param name="peakScalingMzPower" type="float" value="" optional="true" + label="peakScalingMzPower" + help="Intensity scaling power with respect to the m/z value and the raw intensity. The scaled intensity will be (m/z)^mzpow * (raw intensity)^intpow Default is 2.01"/> + <param name="peakScalingIntensityPower" type="float" value="" optional="true" + label="peakScalingIntensityPower" + help="Intensity scaling power with respect to the m/z value and the raw intensity. The scaled intensity will be (m/z)^mzpow * (raw intensity)^intpow Default is 2.01"/> + + <param name="peakScalingUnassignedPeaks" type="float" value="" optional="true" min="0.0" + label="peakScalingUnassignedPeaks" + help="Scaling factor for unassigned peaks in library spectra. Default is 1.0"/> + <param name="peakNoBinning" type="select" optional="true" label="peakNoBinning Default: false" > + <help> Only display the top hit for each query. + </help> + <option value="true">true - Disable binning and perform peak-to-peak matching.</option> + <option value="false">false - Use binning</option> + </param> + <param name="peakBinningNumBinsPerMzUnit" type="integer" value="" optional="true" min="1" + label="peakBinningNumBinsPerMzUnit" + help="Number of bins per Th. Default 1"/> + <param name="peakBinningFractionToNeighbor" type="float" value="" optional="true" + label="peakBinningFractionToNeighbor" + help="Fraction of the scaled intensity assigned to neighboring bins. Default is 0.5"/> + <param name="filterLibMaxPeaksUsed" type="integer" value="" optional="true" min="1" + label="filterLibMaxPeaksUsed" + help="Remove all but the top peaks in the LIBRARY spectra. Default 50"/> + <param name="filterLightIonsMzThreshold" type="integer" value="" optional="true" min="1" + label="filterLightIonsMzThreshold" + help="Remove all light ions with m/z lower than this Th for both library and query spectra. Default 180"/> + <param name="filterITRAQReporterPeaks" type="select" optional="true" label="filterITRAQReporterPeaks Default: false" > + <help> Remove iTRAQ reporter peaks in the range 112-122 Th. + </help> + <option value="true">true - Remove iTRAQ reporter peaks</option> + <option value="false">false - Use binning</option> + </param> + <param name="filterTMTReporterPeaks" type="select" optional="true" label="filterTMTReporterPeaks Default: false" > + <help> Remove TMT reporter peaks in the range 126-132 Th. + </help> + <option value="true">true - Remove TMT reporter peaks</option> + <option value="false">false</option> + </param> + </section> + + <param name="output_format" type="select" label="Output format"> + <option value="pep.xml">pep.xml</option> + <option value="xls">xls (tabular)</option> + <option value="txt">txt (fixed width text)</option> + </param> + <param name="printFingerprintingSummary" type="select" optional="true" label="printFingerprintingSummary Default: no" > + <help> Print a text file summarizing fingerprinting results. + </help> + <option value="fingerprint.summary">yes</option> + </param> + </inputs> + <outputs> + <data name="log" format="txt" label="spectrast.log" from_work_dir="spectrast.log"/> + <data name="params" format="txt" label="spectrast.params" from_work_dir="spectrast.params"/> + <data name="fingerprint_summary" format="txt" label="fingerprint.summary" from_work_dir="fingerprint.summary"> + <filter>printFingerprintingSummary and printFingerprintingSummary == 'fingerprint.summary'</filter> + </data> + <data name="output" format="pep.xml" label="${tool.name} on ${on_string}: ${output_format}"> + <change_format> + <when input="output_format" value="xls" format="tabular" /> + <when input="output_format" value="txt" format="txt" /> + </change_format> + <actions> + <conditional name="output_format"> + <when value="xls"> + <action name="column_names" type="metadata" default="Geneid,${','.join([a.name for a in $input_files])}" /> + </when> + </conditional> + </actions> + </data> + <collection name="output_set" type="list" label="${tool.name} on ${on_string}: ${output_format}"> + <discover_datasets pattern="(?P<designation>.+)\.xls" ext="tabular" directory="out" visible="true" /> + <discover_datasets pattern="__designation_and_ext__" directory="out" visible="true" /> + </collection> + </outputs> + <tests> + <test> + <param name="spectrum_files" value="msgf-test.mzML" ftype="mzml" /> + <param name="libraryFile" value="splib.html" ftype="splib" > + <composite_data value="splib/library.splib"/> + <composite_data value="splib/library.spidx"/> + <composite_data value="splib/library.pepidx"/> + </param> + <param name="output_format" value="xls"/> + <output name="output"> + <assert_contents> + <has_text text="FKWNGTDTNSAAEK" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**SpectraST Search** + +SpectraST_ can perform spectral searching from the following data formats: + + .mzML format + .mzXML (all versions) format + .mzData format + .mgf (Mascot Generic) format + .dta (SEQUEST) format, a simple peak list preceded by precursor information + NIST (National Institute of Standards and Technology)'s .msp format + +The spectral library must be in SpectraST's .splib format, +which can be created in SpectraST Create +or imported from .msp format which can be generated by BiblioSpec_. + +The results can be outputted to the following formats: + .pepXML format + .txt format, a fixed-width column text format + .xls format, a tab-delimited column text format + +.. _SpectraST: http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#SpectraST_Create_Mode +.. _BiblioSpec: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=default + + ]]></help> + <expand macro="citations" /> +</tool>