Mercurial > repos > galaxyp > proteomiqon_psmstatistics

annotate proteomiqon_psmstatistics.xml @ 0:b8590dea5e2d draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
author galaxyp
date Sun, 18 Jul 2021 13:53:08 +0000
parents
children f831f7d721f8
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0
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>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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6 <token name="@VERSION@">0.0.6</token>
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" : $ThresholdCond.MinimumIncreaseBetweenIterations,
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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37 "PepValueFittingMethod" : {
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
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38 "Case":"$ThresholdCond.PepValueFittingMethod"
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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diff changeset
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 <param name="PepValueFittingMethod" type="select" label="Pep-Value fitting method">
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
73 <option value="LinearSpline">Linear Spline</option>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
74 <option value="LogisticRegressionLogit" selected="true">Logistic Regression Logit</option>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
75 </param>
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 <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
78 <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
79 <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
80 </when>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
81 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
82 <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
83 <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
84 </param>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
85 <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
86 </inputs>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
87 <outputs>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
88 <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
89 <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
90 <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
91 </data>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
92 </outputs>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
93 <tests>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
94 <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
95 <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
96 <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
97 <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
98 <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
99 <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
100 <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
101 <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
102 <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
103 <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
104 <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
105 <param name="PepValueFittingMethod" value="LinearSpline"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
106 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
107 </test>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
108 <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
109 <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
110 <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
111 <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
112 <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
113 <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
114 <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
115 <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
116 <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
117 <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
118 <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
119 <param name="PepValueFittingMethod" value="LinearSpline"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
120 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
121 <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
122 </test>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
123 <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
124 <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
125 <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
126 <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
127 <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
128 <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
129 <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
130 <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
131 <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
132 <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
133 <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
134 <param name="PepValueFittingMethod" value="LogisticRegressionLogit"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
135 </conditional>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
136 <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
137 </test>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
parents:
diff changeset
138 <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
139 <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
140 <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
141 <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
142 <param name="outputParamfile" value="true"/>
b8590dea5e2d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 7e7a2e71b21a1c92ae0c79cc4e25a7c2a5f0c4f1"
galaxyp
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143 <conditional name="ThresholdCond">
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144 <param name="ProcessingType" value="Fixed"/>
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145 <param name="SequestLike" value="5.0"/>
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146 <param name="Andromeda" value="40.0"/>
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147 </conditional>
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148 <output name="out_paramfile" file="result_3.json"/>
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149 </test>
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150 </tests>
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151 <help>
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152 <![CDATA[
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153 What It Does
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154 ------------
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155 **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>`_.
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156
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157 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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158
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159 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.
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160 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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161 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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162
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163 .. image:: SemiSupervisedScoring.png
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164 :width: 768pt
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165 :height: 345pt
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166
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167 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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168 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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169
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170 Further Reading
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171 ---------------
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172 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html>`_.
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173 ]]>
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174 </help>
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175 </tool>