Mercurial > repos > galaxyp > encyclopedia_quantify
changeset 0:4081e4faa4ab draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
| author | galaxyp |
|---|---|
| date | Mon, 14 Sep 2020 17:06:06 +0000 |
| parents | |
| children | 1c5cbf8f79ce |
| files | encyclopedia_quantify.xml macros.xml static/images/SearchToLib_Workflow.png |
| diffstat | 3 files changed, 698 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/encyclopedia_quantify.xml Mon Sep 14 17:06:06 2020 +0000 @@ -0,0 +1,147 @@ +<tool id="encyclopedia_quantify" name="EncyclopeDIA Quantify" version="@VERSION@.0"> + <description>samples from Data-Independent Acquisition (DIA) MS/MS Data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + @SEARCH2LIB_CMDS@ + ]]></command> + <inputs> + <expand macro="scan_inputs"/> + <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/> + <expand macro="fasta_input"/> + <expand macro="target_fasta"/> + <expand macro="options_section"/> + <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/> + <param name="select_outputs" type="select" label="Select outputs" multiple="true"> + <option value="log" selected="true">log</option> + <option value="elib" selected="true">elib</option> + <option value="features" selected="false">concatenated_features.txt</option> + <option value="results" selected="true">concatenated_results.txt</option> + <option value="decoy" selected="false">concatenated_decoy.txt</option> + <option value="rt_plots" selected="false">Retention Time Plots</option> + <option value="rt_tables" selected="false">Retention Time Tables</option> + <option value="peptides" selected="true">peptides.txt (requires align between files)</option> + <option value="proteins" selected="true">proteins.txt (requires align between files)</option> + </param> + </inputs> + <outputs> + <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log"> + <filter>'log' in select_outputs</filter> + </data> + <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib"> + <filter>'elib' in select_outputs</filter> + </data> + <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt"> + <filter>'features' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" /> + </actions> + </data> + <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt"> + <filter>'results' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> + </actions> + </data> + <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt"> + <filter>'decoy' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> + </actions> + </data> + <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots"> + <filter>library and 'rt_plots' in select_outputs</filter> + <discover_datasets pattern="(?P<designation>.+\.pdf)" ext="pdf" directory="inputs"/> + </collection> + <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables"> + <filter>library and 'rt_tables' in select_outputs</filter> + <discover_datasets pattern="(?P<designation>.+\.mzML\..+\.rt_fit\.txt)" ext="tabular" directory="inputs"/> + </collection> + <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt"> + <filter>a and 'peptides' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> + </actions> + </data> + <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.elib.proteins.txt"> + <filter>a and 'proteins' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="scan_inputs" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML,BCS_hela_wide_500_900_2.mzML"/> + <param name="library" ftype="elib" value="BCS_hela.elib"/> + <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/> + <output name="results" ftype="tabular"> + <assert_contents> + <has_text text="GIEQAVQSHAVAEEEAR"/> + </assert_contents> + </output> + <output name="peptides" ftype="tabular"> + <assert_contents> + <has_text text="AYPLADAHLTK"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +**EncyclopeDIA Quantify** + +@ENCYCLOPEDIA_WIKI@ + +EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results. + + +**Inputs** + + - Spectrum files in mzML format + - A chromatogram library that can be generated by SearchToLib + - A protein data base in fasta format + +@MSCONVERT_HELP@ + +**Outputs** + + - A log file + - A Chromatogram Library (.elib) + - The identified features in tabular format + Feature values of scans that are used by percolator to determine matches. + - The identified Peptide Spectral Match results in tabular format + Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds + - The identified peptides in tabular format + Per peptide: the normalized intensity for each scan file. + Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ... + - The identified proteins in tabular format + Per protein: the normalized intensity for each scan file. + Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ... + + +**Typical DIA SearchToLib Workflow** + +Two sets of Mass Spec MS/MS DIA data are collected for the experiment. In addition to collecting wide-window DIA experiments on each quantitative replicate, a pool containing peptides from every condition is measured using several staggered narrow-window DIA experiments. + + 1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library. + If a Spectral library argument is provided, for example from **Prosit**, SearchToLIB uses EncyclopeDIA to search each input spectrum mzML file. + Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring. + + + * Prosit_ generates a predicted spectrum library of fragmentation patterns and retention times for every +2H and +3H tryptic peptide in a FASTA database, with up to one missed cleavage. + + + 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library, with the *align between files* option, to produce quantification results. + +.. image:: SearchToLib_Workflow.png + :width: 810 + :height: 580 + +.. _Prosit: https://www.proteomicsdb.org/prosit + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 14 17:06:06 2020 +0000 @@ -0,0 +1,551 @@ +<macros> + <token name="@VERSION@">0.9.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">encyclopedia</requirement> + <yield/> + </requirements> + </xml> + + <token name="@ENCYCLOPEDIA_WIKI@"> +EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home + +.. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41467-018-07454-w</citation> + <citation type="doi">10.1038/s41467-020-15346-1</citation> + <citation type="doi">10.1074/mcp.P119.001913</citation> + <yield/> + </citations> + </xml> + + <token name="@CMD_IMPORTS@"> +#import re +#def identifier_or_name($input1) + #if hasattr($input1, 'element_identifier') + #return $input1.element_identifier + #else + #return $input1.name + #end if +#end def +#def clean($name1) + #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) + #return $name_clean +#end def +#def ln_name($ds) + #set $ext = '' + #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') + #set $ext = ".mzML" + #else if $ds.is_of_type('elib') + #set $ext = ".elib" + #else if $ds.is_of_type('dlib') + #set $ext = ".dlib" + #else if $ds.is_of_type('blib') + #set $ext = ".blib" + #else if $ds.is_of_type('fasta') + #set $ext = ".fasta" + #else if $ds.is_of_type('fasta.gz') + #set $ext = ".fasta.gz" + #end if + #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) + #return $name +#end def +#set $i_name = None +#set $f_name = None +#set $l_name = None +#set $t_name = None + </token> + + <xml name="scan_input"> + <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format"> + <help>@MSCONVERT_RAW@</help> + </param> + </xml> + <token name="@LINK_SCAN_INPUT@"><![CDATA[ + #set $i_name = $ln_name($scan_input) + ln -s '$scan_input' '$i_name' && + ]]></token> + <token name="@SCAN_INPUT@"> + -i '$i_name' + </token> + + <xml name="scan_inputs"> + <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format"> + <help>@MSCONVERT_RAW@</help> + </param> + </xml> + <token name="@LINK_SCAN_INPUTS@"><![CDATA[ + #set $inputs_dir = 'inputs' + mkdir -p $inputs_dir && + #for $sf in $scan_inputs + #set $i_name = $ln_name($sf) + ln -s '$sf' '${inputs_dir}/${i_name}' && + #end for + ]]></token> + <token name="@SCAN_INPUTS@"> + -i '$inputs_dir' + </token> + + <xml name="fasta_input"> + <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database"> + <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help> + </param> + </xml> + <token name="@LINK_FASTA_INPUT@"><![CDATA[ + #set $f_name = $ln_name($fasta) + ln -s '$fasta' '$f_name' && + ]]></token> + <token name="@FASTA_INPUT@"> + -f '$f_name' + </token> + + <xml name="target_fasta"> + <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"> + <help>Optional - Only analyze this subset of the background fasta proteome</help> + </param> + <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides"> + <help>Rather than full proteins</help> + </param> + </xml> + <token name="@LINK_TARGET_FASTA@"><![CDATA[ + #if $target_fasta + #set $t_name = $ln_name($target_fasta) + ln -s '$target_fasta' '$t_name' && + #else + #set $t_name = None + #end if + ]]></token> + <token name="@TARGET_FASTA@"> + #if $t_name + -t '$t_name' + -tp $tp + #end if + </token> + + <xml name="lib_input" token_optional="true" token_libhelp=""> + <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> + <help>@LIBHELP@</help> + </param> + </xml> + <token name="@LINK_LIB_INPUT@"><![CDATA[ + #if $library + #set $l_name = $ln_name($library) + cp '$library' '$l_name' && + #else + #set $l_name = None + #end if + ]]></token> + <token name="@LIB_INPUT@"> + #if $l_name + -l '$l_name' + #end if + </token> + + <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false" + token_cid_selected="false" token_hcd_selected="false"> + <conditional name="acquisition"> + <param name="set_acquisition" type="select" label="Set Acquisition Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/> + <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type"> + <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option> + <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option> + </param> + <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme"> + <option value="Trypsin">Trypsin</option> + <option value="Trypsin/p">Trypsin/p</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="Arg-C">Arg-C</option> + <option value="Glu-C">Glu-C</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Pepsin A">Pepsin A</option> + <option value="Elastase">Elastase</option> + <option value="Thermolysin">Thermolysin</option> + <option value="No Enzyme">No Enzyme</option> + </param> + <param argument="-frag" type="select" optional="true" label="Fragmentation"> + <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option> + <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option> + <option value="ETD">ETD (C/Z/Z+1)</option> + </param> + </when> + </conditional> + </xml> + <xml name="encyclopedia_common_options"> + <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false" + token_cid_selected="true" token_hcd_selected="false"/> + </xml> + <xml name="walnut_common_options"> + <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true" + token_cid_selected="false" token_hcd_selected="true"/> + </xml> + <token name="@COMMON_OPTIONS@"> + #if $options.acquisition.set_acquisition == 'yes' + -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched + #if $options.acquisition.acquisition + -acquisition '$options.acquisition.acquisition' + #end if + #if $options.acquisition.enzyme: + -enzyme '$options.acquisition.enzyme' + #end if + #if $options.acquisition.frag: + -frag '$options.acquisition.frag' + #end if + #end if + </token> + + <xml name="mass_tolerance"> + <conditional name="tolerance"> + <param name="set_tolerance" type="select" label="Set Tolerance Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <conditional name="precursor_tolerance"> + <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance"> + <option value="PPM">PPM</option> + <option value="AMU">AMU</option> + <option value="Resolution">Resolution</option> + </param> + <when value="PPM"> + <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/> + </when> + <when value="AMU"> + <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/> + </when> + <when value="Resolution"> + <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/> + </when> + </conditional> + <conditional name="fragment_tolerance"> + <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance"> + <option value="PPM">PPM</option> + <option value="AMU">AMU</option> + <option value="Resolution">Resolution</option> + </param> + <when value="PPM"> + <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/> + </when> + <when value="AMU"> + <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/> + </when> + <when value="Resolution"> + <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/> + </when> + </conditional> + <yield/> + </when> + </conditional> + </xml> + <token name="@MASS_TOLERANCE@"> + #if $options.tolerance.set_tolerance == 'yes' + -ptolunits $options.tolerance.precursor_tolerance.ptolunits + -ptol $options.tolerance.precursor_tolerance.ptol + -ftolunits $options.tolerance.fragment_tolerance.ftolunits + -ftol $options.tolerance.fragment_tolerance.ftol + #end if + </token> + + <xml name="mass_library_tolerance"> + <expand macro="mass_tolerance"> + <conditional name="library_tolerance"> + <param argument="-ltolunits" type="select" label="Library Mass Tolerance"> + <option value="defaults">Use defaults</option> + <option value="PPM">PPM</option> + <option value="AMU">AMU</option> + <option value="Resolution">Resolution</option> + </param> + <when value="defaults"/> + <when value="PPM"> + <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/> + </when> + <when value="AMU"> + <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/> + </when> + <when value="Resolution"> + <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/> + </when> + </conditional> + </expand> + </xml> + <token name="@MASS_LIBRARY_TOLERANCE@"> + @MASS_TOLERANCE@ + #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults' + -ltolunits $options.tolerance.library_tolerance.ltolunits + -ltol $options.tolerance.library_tolerance.ltol + #end if + </token> + + <xml name="percolator_options"> + <conditional name="percolator"> + <param name="set_percolator" type="select" label="Set Percolator Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/> + <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/> + <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> + </when> + </conditional> + </xml> + <token name="@PERCOLATOR_OPTIONS@"> + #if $options.percolator.set_percolator == 'yes' + #if str($options.percolator.percolatorVersionNumber) + -percolatorVersionNumber $options.percolator.percolatorVersionNumber + #end if + #if str($options.percolator.percolatorProteinThreshold) + -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold + #end if + #if str($options.percolator.percolatorThreshold) + -percolatorThreshold $options.percolator.percolatorThreshold + #end if + #end if + </token> + + <xml name="peak_options"> + <conditional name="peak"> + <param name="set_peak" type="select" label="Set Peak Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/> + <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/> + <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/> + <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/> + <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/> + <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + </when> + </conditional> + </xml> + <token name="@PEAK_OPTIONS@"> + #if $options.peak.set_peak == 'yes' + #if str($options.peak.numberOfQuantitativePeaks) + -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks + #end if + #if str($options.peak.minNumOfQuantitativePeaks) + -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks + #end if + #if str($options.peak.minQuantitativeIonNumber) + -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber + #end if + #if str($options.peak.minIntensity) + -minIntensity $options.peak.minIntensity + #end if + #if str($options.peak.expectedPeakWidth) + -expectedPeakWidth $options.peak.expectedPeakWidth + #end if + #if $options.peak.filterPeaklists + -filterPeaklists $options.peak.filterPeaklists + #end if + #end if + </token> + + <xml name="window_options"> + <conditional name="window"> + <param name="set_window" type="select" label="Set Window Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/> + <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/> + <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/> + <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/> + <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/> + <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType"> + <option value="window">Across entire window</option> + <option value="recal20">Recalibrated (20% gradient)</option> + <option value="recal">Recalibrated (peak width only)</option> + <option value="uncal20">Uncalibrated (20% gradient)</option> + <option value="uncal">Uncalibrated (peak width only)</option> + </param> + </when> + </conditional> + </xml> + <token name="@WINDOW_OPTIONS@"> + #if $options.window.set_window == 'yes' + #if str($options.window.foffset) + -foffset $options.window.foffset + #end if + #if str($options.window.poffset) + -poffset $options.window.poffset + #end if + #if str($options.window.precursorIsolationMargin) + -precursorIsolationMargin $options.window.precursorIsolationMargin + #end if + #if str($options.window.precursorWindowSize) + -precursorWindowSize $options.window.precursorWindowSize + #end if + #if str($options.window.rtWindowInMin) + -rtWindowInMin $options.window.rtWindowInMin + #end if + #if $options.window.scoringBreadthType + -scoringBreadthType $options.window.scoringBreadthType + #end if + #end if + </token> + + <xml name="modification_options"> + <conditional name="modifications"> + <param name="set_modifications" type="select" label="Set Modifications Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-fixed" type="select" optional="true" label="Fixed Modification"> + <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option> + <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option> + <option value="C=45.987721">C+46 (MMTS) C=45.987721</option> + <option value="C=125.047679">C+125 (NEM) C=125.047679</option> + </param> + <yield/> + <!-- + <param argument="-localizationModification" type="select" optional="true" label="localizationModification"> + </param> + --> + <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> + </when> + </conditional> + </xml> + <token name="@MODIFICATION_OPTIONS@"> + #if $options.modifications.set_modifications == 'yes' + #if $options.modifications.fixed + -fixed $options.modifications.fixed + #end if + -verifyModificationIons $options.modifications.verifyModificationIons + #end if + </token> + + <xml name="search_options"> + <conditional name="search"> + <param name="set_search" type="select" label="Set Search Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/> + <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/> + <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/> + <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/> + <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/> + <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/> + <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/> + <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/> + <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/> +<!-- + <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/> + <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/> +--> + </when> + </conditional> + </xml> + <token name="@SEARCH_OPTIONS@"> + #if $options.search.set_search == 'yes' + -minCharge $options.search.minCharge + -maxCharge $options.search.maxCharge + -minLength $options.search.minLength + -maxLength $options.search.maxLength + -minEluteTime $options.search.minEluteTime + -maxMissedCleavage $options.search.maxMissedCleavage + -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber + -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks + -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks + ## -addDecoysToBackground $options.search.addDecoysToBackground + ## -dontRunDecoys $options.search.dontRunDecoys + #end if + </token> + + <xml name="options_section"> + <section name="options" title="Parameter Settings" expanded="false"> + <expand macro="common_options"/> + <expand macro="mass_library_tolerance"/> + <expand macro="percolator_options"/> + <expand macro="peak_options"/> + <expand macro="window_options"/> + <expand macro="modification_options"/> + <expand macro="search_options"/> + </section> + </xml> + + <xml name="libexport"> + <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> + </xml> + + <token name="@SEARCH2LIB_CMDS@"><![CDATA[ + @CMD_IMPORTS@ + @LINK_SCAN_INPUTS@ + @LINK_FASTA_INPUT@ + @LINK_TARGET_FASTA@ + @LINK_LIB_INPUT@ + for SCAN_FILE in `ls -1 inputs/*`; do + echo "\$SCAN_FILE" && + EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US + -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g + -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}" + #if not $library + -walnut + #end if + -i \$SCAN_FILE + @FASTA_INPUT@ + @TARGET_FASTA@ + @LIB_INPUT@ + @COMMON_OPTIONS@ + @MASS_LIBRARY_TOLERANCE@ + @PERCOLATOR_OPTIONS@ + @PEAK_OPTIONS@ + @WINDOW_OPTIONS@ + @MODIFICATION_OPTIONS@ + @SEARCH_OPTIONS@ | tee -a search2lib.log + ; done && + for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done && + EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport + #if not $library + -pecan + #end if + @SCAN_INPUTS@ + @FASTA_INPUT@ + @TARGET_FASTA@ + @LIB_INPUT@ + -a $a + -o chromatogram_library.elib + && ls -l ./*.* inputs/* + | tee -a search2lib.log +]]> + </token> + <token name="@MSCONVERT_CMD@"><![CDATA[ + msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw +]]> + </token> + <token name="@MSCONVERT_RAW@"><![CDATA[ +mzML conversion from RAW requires special options: @MSCONVERT_CMD@ +]]> + </token> + <token name="@MSCONVERT_HELP@"><![CDATA[ + + The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options: + + :: + + @MSCONVERT_CMD@ + +]]> + </token> +</macros>