Mercurial > repos > galaxyp > proteomiqon_psmstatistics

annotate proteomiqon_psmstatistics.xml @ 1:f831f7d721f8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 28244fe226c9bd5326886bf21960cbb43a4be2ec"
author galaxyp
date Fri, 27 Aug 2021 07:28:43 +0000
parents b8590dea5e2d
children 9ac2e8232c5c
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b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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1 <tool id="proteomiqon_psmstatistics" name="ProteomIQon PSMStatistics" version="@VERSION@" profile="20.05">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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2 <description>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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3 utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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4 </description>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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5 <macros>
1
f831f7d721f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 28244fe226c9bd5326886bf21960cbb43a4be2ec"
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6 <token name="@VERSION@">0.0.7</token>
0
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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7 </macros>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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8 <requirements>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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9 <requirement type="package" version="@VERSION@">proteomiqon-psmstatistics</requirement>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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10 </requirements>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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11 <command detect_errors="exit_code"><![CDATA[
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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12 #import re
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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13 #set basename = $re.sub(r'[^\w ,.\-+]','_', $psm.element_identifier)
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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14 #if $outputParamfile:
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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15 cat '$paramfile' >> '$out_paramfile' &&
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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16 #end if
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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17 ln -s '$psm' '${basename}.psm' &&
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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18 ln -s '$out_qpsm' '${basename}.qpsm' &&
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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19 proteomiqon-psmstatistics -i './${basename}.psm' -d '$peptideDB' -p '$paramfile' -o ./
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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20 ]]>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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21 </command>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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22 <configfiles>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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23 <configfile name="paramfile">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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24 <![CDATA[
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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25 {
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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26 "Threshold":
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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27 {
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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28 #if $ThresholdCond.ProcessingType == "Estimate"
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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29 "Case":"Estimate",
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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30 "Fields":
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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31 [
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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32 {
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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33 "QValueThreshold" : $ThresholdCond.QValueThreshold,
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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34 "PepValueThreshold" : $ThresholdCond.PepValueThreshold,
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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35 "MaxIterations" : $ThresholdCond.MaxIterations,
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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36 "MinimumIncreaseBetweenIterations" : $ThresholdCond.MinimumIncreaseBetweenIterations,
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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37 "PepValueFittingMethod" : {
1
f831f7d721f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 28244fe226c9bd5326886bf21960cbb43a4be2ec"
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38 "Case":"LinearLogit"
0
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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39 }
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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40 }
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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41 ]
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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42 #else if $ThresholdCond.ProcessingType == "Fixed"
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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43 "Case":"Fixed",
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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44 "Fields":
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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45 [
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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46 {
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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47 "SequestLike":$ThresholdCond.SequestLike,
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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48 "Andromeda":$ThresholdCond.Andromeda
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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49 }
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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50 ]
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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51 #end if
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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52 },
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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53 "ParseProteinIDRegexPattern":"${ParseProteinIDRegexPattern}",
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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54 "KeepTemporaryFiles":false
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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55 }
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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56 ]]>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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57 </configfile>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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58 </configfiles>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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59 <inputs>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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60 <param name="psm" type="data" format="tabular" label="PSM" help="Specify list of peptide spectrum matches to be scored."/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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61 <param name="peptideDB" type="data" format="sqlite" label="Peptide database" help="Specify the peptide data base."/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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62 <conditional name="ThresholdCond">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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63 <param name="ProcessingType" type="select" label="Processing type" help="Specify how PSM thresholds should be estimated using semi supervised machine learning techniques (recommended) or if fixed score values should be used instead.">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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64 <option value="Estimate" selected="true">Estimate</option>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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65 <option value="Fixed">Fixed</option>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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66 </param>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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67 <when value="Estimate">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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68 <param name="QValueThreshold" type="float" value="0.01" label="Q-Value threshold" />
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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69 <param name="PepValueThreshold" type="float" value="0.05" label="Pep-Value threshold" />
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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70 <param name="MaxIterations" type="integer" value="15" label="Max iterations" />
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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71 <param name="MinimumIncreaseBetweenIterations" type="float" value="0.005" label="Minimum increase between iterations" />
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
72 </when>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
73 <when value="Fixed">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
74 <param name="SequestLike" type="float" value="5.0" label="Sequest like" />
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
75 <param name="Andromeda" type="float" value="40.0" label="Andromeda" />
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
76 </when>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
77 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
78 <param name="ParseProteinIDRegexPattern" type="text" value="id" label="Parse protein ID regex pattern" help="Fasta headers do often contain additional information in addition to your protein identifier, by specifying a regex pattern the tool can extract the protein IDs. If you fasta headers are already cleaned you can leave this field empty.">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
79 <sanitizer sanitize="false" />
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
80 </param>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
81 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
82 </inputs>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
83 <outputs>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
84 <data format="tabular" name="out_qpsm" />
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
85 <data format="json" name="out_paramfile">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
86 <filter>outputParamfile</filter>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
87 </data>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
88 </outputs>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
89 <tests>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
90 <test expect_num_outputs="1">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
91 <param name="psm" value="sample.psm"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
92 <param name="peptideDB" value="sample.db"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
93 <param name="ParseProteinIDRegexPattern" value="id"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
94 <param name="outputParamfile" value="false"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
95 <conditional name="ThresholdCond">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
96 <param name="ProcessingType" value="Estimate"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
97 <param name="QValueThreshold" value="0.01"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
98 <param name="PepValueThreshold" value="0.05"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
99 <param name="MaxIterations" value="15"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
100 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
101 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
102 </test>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
103 <test expect_num_outputs="2">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
104 <param name="psm" value="sample.psm"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
105 <param name="peptideDB" value="sample.db"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
106 <param name="ParseProteinIDRegexPattern" value="id"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
107 <param name="outputParamfile" value="true"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
108 <conditional name="ThresholdCond">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
109 <param name="ProcessingType" value="Estimate"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
110 <param name="QValueThreshold" value="0.01"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
111 <param name="PepValueThreshold" value="0.05"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
112 <param name="MaxIterations" value="15"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
113 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
114 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
115 <output name="out_paramfile" file="result_1.json"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
116 </test>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
117 <test expect_num_outputs="2">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
118 <param name="psm" value="sample.psm"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
119 <param name="peptideDB" value="sample.db"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
120 <param name="ParseProteinIDRegexPattern" value="id"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
121 <param name="outputParamfile" value="true"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
122 <conditional name="ThresholdCond">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
123 <param name="ProcessingType" value="Estimate"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
124 <param name="QValueThreshold" value="0.01"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
125 <param name="PepValueThreshold" value="0.05"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
126 <param name="MaxIterations" value="15"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
127 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
128 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
129 <output name="out_paramfile" file="result_2.json"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
130 </test>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
131 <test expect_num_outputs="2">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
132 <param name="psm" value="sample.psm"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
133 <param name="peptideDB" value="sample.db"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
134 <param name="ParseProteinIDRegexPattern" value="id"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
135 <param name="outputParamfile" value="true"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
136 <conditional name="ThresholdCond">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
137 <param name="ProcessingType" value="Fixed"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
138 <param name="SequestLike" value="5.0"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
139 <param name="Andromeda" value="40.0"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
140 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
141 <output name="out_paramfile" file="result_3.json"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
142 </test>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
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143 </tests>
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144 <help>
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145 <![CDATA[
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146 What It Does
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147 ------------
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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148 **Disclaimer** Disclaimer this tool needs a `peptide database <https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html>`_ and `peptide spectrum matches <https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html>`_.
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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149
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150 An established method to identify acquired MS/MS spectra is the comparison of each spectrum with peptides in a reference database.
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151
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152 To measure the similarity of in silico generated spectra and measured MS/MS scans we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem.
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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153 Additionally, we also record quality control parameters such as the mass difference between the precursor ion and the theoretically calulated mass or the uniquness of each score in comparison to 'competing' peptides within the search space.
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154 The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.
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155
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156 .. image:: SemiSupervisedScoring.png
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157 :width: 768pt
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158 :height: 345pt
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159
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160 Since the search space is extended by so called decoys - reversed counterparts of peptides within the search space - we can estimate the distribution of 'true negatives' and calculate local (PEP values) and global (Q values) false discovery rates at each consensus score.
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161 The reported peptides at user defined local and global FDR cutoffs can then be used as inputs for any downstream analysis be it ProteinInference or PSMBasedQuantification.
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162
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163 Further Reading
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164 ---------------
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165 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html>`_.
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166 ]]>
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167 </help>
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168 </tool>