Mercurial > repos > galaxyp > proteomiqon_peptidespectrummatching

annotate proteomiqon_peptidespectrummatching.xml @ 0:db6faafbf75b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
author galaxyp
date Thu, 15 Jul 2021 07:11:01 +0000
parents
children a79a24eb9e76
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db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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1 <tool id="proteomiqon_peptidespectrummatching" name="ProteomIQon PeptideSpectrumMatching" version="@VERSION@" profile="20.05">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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2 <description>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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3 iterates across all MS/MS scans in an MS run, determines precursor charge states and possible peptide spectrum matches.
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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4 </description>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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5 <macros>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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6 <token name="@VERSION@">0.0.7</token>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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7 </macros>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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8 <requirements>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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9 <requirement type="package" version="@VERSION@">proteomiqon-peptidespectrummatching</requirement>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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10 </requirements>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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11 <command detect_errors="exit_code"><![CDATA[
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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12 #import re
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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13 #set basename = $re.sub(r'[^\w ,.\-+]','_',$instrumentOutput.element_identifier)
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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14 #if $outputParamfile:
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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15 cat '$paramfile' >> '$out_paramfile' &&
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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16 #end if
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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17 ln -s '$instrumentOutput' '${basename}.mzlite' &&
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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18 ln -s '$out_psm' '${basename}.psm' &&
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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19 proteomiqon-peptidespectrummatching -i './${basename}.mzlite' -d '$peptideDB' -p '$paramfile' -o ./
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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20 ]]>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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21 </command>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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22 <configfiles>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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23 <configfile name="paramfile">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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24 <![CDATA[
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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25 {
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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26 "ChargeStateDeterminationParams": {
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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27 "ExpectedMinimalCharge": ${ChargeStateDeterminationParams.ExpectedMinimalCharge},
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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28 "ExpectedMaximumCharge": ${ChargeStateDeterminationParams.ExpectedMaximumCharge},
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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29 "Width": ${ChargeStateDeterminationParams.Width},
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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30 "MinIntensity": ${ChargeStateDeterminationParams.MinIntensity},
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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31 "DeltaMinIntensity": ${ChargeStateDeterminationParams.DeltaMinIntensity},
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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32 "NrOfRndSpectra": ${ChargeStateDeterminationParams.NrOfRndSpectra}
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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33 },
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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34 "LookUpPPM": ${LookUpPPM},
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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35 "nTerminalSeries": { "Case": "${nTerminalSeries}" },
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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36 "cTerminalSeries": { "Case": "${cTerminalSeries}" },
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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37 "Andromeda": {
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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38 "PMinPMax": {
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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39 "Item1": ${Andromeda.PMin},
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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40 "Item2": ${Andromeda.PMax}
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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41 },
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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42 "MatchingIonTolerancePPM": ${Andromeda.MatchingIonTolerancePPM}
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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43 }
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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44 }
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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45 ]]>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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46 </configfile>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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47 </configfiles>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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48 <inputs>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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49 <param name="instrumentOutput" type="data" format="sqlite" label="Instrument output" help="Specify mass spectrometry data you want to analyze."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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50 <param name="peptideDB" type="data" format="sqlite" label="Peptide database" help="Specify the peptide data base."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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51 <section name="ChargeStateDeterminationParams" title="Charge state determination parameters" >
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52 <param name="ExpectedMinimalCharge" type="integer" min="1" max="8" value="2" label="Expected minimal charge" help="Specify the minimum peptide ion charge state to consider."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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53 <param name="ExpectedMaximumCharge" type="integer" min="1" max="8" value="5" label="Expected maximum charge" help="Specify the maximum peptide ion charge state to consider."/>
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54 <param name="Width" type="float" value="1.1" label="Width" help="Specify the width around the picked precursor ion used in charge state determination."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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55 <param name="MinIntensity" type="float" value="0.15" label="Min intensity" help="Specify minimum relative intensity within an putative isotopic envelope to be included when performing charge state determination."/>
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56 <param name="DeltaMinIntensity" type="float" value="0.3" label="Delta min intensity" help="Specify minimum relative intensity to the prior peak when iterating through peak lists while performing charge state determination."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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57 <param name="NrOfRndSpectra" type="integer" value="10000" label="Number of random spectra" help="When performing charge state determination we compared measured envelopes to the distribution of randomly generated spectra. This parameter tunes the size of the generated data set."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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58 </section>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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59 <param name="LookUpPPM" type="float" value="30" label="Lookup PPM" help="Specify the width of the search space when retrieving in silico generated peptide ions from the peptide data base. The width is calculated relative to the precursor mz in ppm."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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60 <param name="nTerminalSeries" type="select" optional="false" label="N-terminal series" help="Specify the types of N-terminal charged ion fragments included in the generation of in silico fragment spectra." multiple="true" display="checkboxes">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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61 <option value="A">A</option>
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62 <option value="B" selected="true">B</option>
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63 <option value="C">C</option>
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64 </param>
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65 <param name="cTerminalSeries" type="select" optional="false" label="C-terminal Series" help="Specify the types of C-terminal charged ion fragments included in the generation of in silico fragment spectra." multiple="true" display="checkboxes">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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66 <option value="X">X</option>
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67 <option value="Y" selected="true">Y</option>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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68 <option value="Z">Z</option>
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69 </param>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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70 <section name="Andromeda" title="Andromeda">
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71 <param name="PMin" type="integer" value="4" label="P min" help="Specify the minimum N of the top N most abundand peaks within a 100 Da window used to compute the Andromeda score."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
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diff changeset
72 <param name="PMax" type="integer" value="10" label="P max" help="Specify the maximum N of the top N most abundand peaks within a 100 Da window used to compute the Andromeda score."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
73 <param name="MatchingIonTolerancePPM" type="float" value="100.0" label="Matching ion tolerance PPM" help="Specify the minimum m/z difference between a measured and an in silico generated peak during peak matching. The width is calculated relative to the m/z of the measured peak in ppm."/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
74 </section>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
75 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
76 </inputs>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
77 <outputs>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
78 <data format="tabular" name="out_psm" />
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
79 <data format="json" name="out_paramfile">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
80 <filter>outputParamfile</filter>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
81 </data>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
82 </outputs>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
83 <tests>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
84 <test expect_num_outputs="1">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
85 <param name="instrumentOutput" value="sample.mzlite"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
86 <param name="peptideDB" value="sample.db"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
87 <param name="LookUpPPM" value="30"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
88 <param name="nTerminalSeries" value="A"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
89 <param name="cTerminalSeries" value="X"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
90 <section name="ChargeStateDeterminationParams">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
91 <param name="ExpectedMinimalCharge" value="2"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
92 <param name="ExpectedMaximumCharge" value="5"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
93 <param name="Width" value="1.1"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
94 <param name="MinIntensity" value="0.15"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
95 <param name="DeltaMinIntensity" value="0.3"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
96 <param name="NrOfRndSpectra" value="10000"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
97 </section>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
98 <section name="Andromeda">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
99 <param name="PMin" value="4"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
100 <param name="PMax" value="10"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
101 <param name="MatchingIonTolerancePPM" value="100.0"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
102 </section>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
103 <param name="outputParamfile" value="false"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
104 </test>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
105 <test expect_num_outputs="2">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
106 <param name="instrumentOutput" value="sample.mzlite"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
107 <param name="peptideDB" value="sample.db"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
108 <param name="LookUpPPM" value="30"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
109 <param name="nTerminalSeries" value="B"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
110 <param name="cTerminalSeries" value="Y"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
111 <section name="ChargeStateDeterminationParams">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
112 <param name="ExpectedMinimalCharge" value="2"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
113 <param name="ExpectedMaximumCharge" value="5"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
114 <param name="Width" value="1.1"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
115 <param name="MinIntensity" value="0.15"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
116 <param name="DeltaMinIntensity" value="0.3"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
117 <param name="NrOfRndSpectra" value="10000"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
118 </section>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
119 <section name="Andromeda">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
120 <param name="PMin" value="4"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
121 <param name="PMax" value="10"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
122 <param name="MatchingIonTolerancePPM" value="100.0"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
123 </section>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
124 <param name="outputParamfile" value="true"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
125 <output name="out_paramfile" file="result_1.json"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
126 </test>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
127 <test expect_num_outputs="2">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
128 <param name="instrumentOutput" value="sample.mzlite"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
129 <param name="peptideDB" value="sample.db"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
130 <param name="LookUpPPM" value="30"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
131 <param name="nTerminalSeries" value="A"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
132 <param name="cTerminalSeries" value="Z"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
133 <section name="ChargeStateDeterminationParams">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
134 <param name="ExpectedMinimalCharge" value="2"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
135 <param name="ExpectedMaximumCharge" value="5"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
136 <param name="Width" value="1.1"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
137 <param name="MinIntensity" value="0.15"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
138 <param name="DeltaMinIntensity" value="0.3"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
139 <param name="NrOfRndSpectra" value="10000"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
140 </section>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
141 <section name="Andromeda">
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
142 <param name="PMin" value="4"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
143 <param name="PMax" value="10"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
144 <param name="MatchingIonTolerancePPM" value="100.0"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
145 </section>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
146 <param name="outputParamfile" value="true"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
diff changeset
147 <output name="out_paramfile" file="result_2.json"/>
db6faafbf75b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
galaxyp
parents:
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148 </test>
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149 <test expect_num_outputs="2">
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150 <param name="instrumentOutput" value="sample.mzlite"/>
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151 <param name="peptideDB" value="sample.db"/>
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152 <param name="LookUpPPM" value="30"/>
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153 <param name="nTerminalSeries" value="C"/>
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154 <param name="cTerminalSeries" value="X"/>
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155 <section name="ChargeStateDeterminationParams">
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156 <param name="ExpectedMinimalCharge" value="2"/>
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157 <param name="ExpectedMaximumCharge" value="5"/>
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158 <param name="Width" value="1.1"/>
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159 <param name="MinIntensity" value="0.15"/>
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160 <param name="DeltaMinIntensity" value="0.3"/>
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161 <param name="NrOfRndSpectra" value="10000"/>
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162 </section>
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163 <section name="Andromeda">
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164 <param name="PMin" value="4"/>
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165 <param name="PMax" value="10"/>
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166 <param name="MatchingIonTolerancePPM" value="100.0"/>
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167 </section>
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168 <param name="outputParamfile" value="true"/>
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169 <output name="out_paramfile" file="result_3.json"/>
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170 </test>
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171 </tests>
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172 <help>
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173 <![CDATA[
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174 What It Does
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175 ------------
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176 **Disclaimer** this tool needs a peptide database to query against, if you did not create one yet you can do so by using the `PeptideDB <https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html>`_ tool.
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177
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178 Given raw a MS run in the mzite format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor ions which were selected for fragmentation.
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179 With this it is possible to query the peptide data base for every precursor ion mass +/- a tolerance (which defines the so called 'search space') and retrieve peptides that are
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180 theoretical candidates for a match. For each of the peptide candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan.
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181
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182 .. image:: PSM.png
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183 :width: 768pt
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184 :height: 563pt
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185
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186 To measure similarity we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem.
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187 The search space is extended by so called decoys. Decoys are reversed counterparts of peptides within the search space and allow
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188 us to assign a false discovery rate to each scored peptide using the `PSMStatistics <https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html>`_ tool.
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189
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190 Further Reading
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191 ---------------
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192 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html>`_.
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193 ]]>
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194 </help>
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195 </tool>