Mercurial > repos > galaxyp > proteomiqon_psmbasedquantification

annotate proteomiqon_psmbasedquantification.xml @ 0:65ce27f0fa01 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
author galaxyp
date Fri, 10 Sep 2021 05:41:32 +0000
parents
children 4abcc674fc0b
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65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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1 <tool id="proteomiqon_psmbasedquantification" name="Proteomiqon PSMBasedQuantification" version="@VERSION@" profile="20.05">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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2 <description>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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3 allows label-free quantification as well as quantification of full metabolic labeled samples.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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4 </description>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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5 <macros>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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6 <token name="@VERSION@">0.0.7</token>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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7 </macros>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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8 <requirements>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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9 <requirement type="package" version="@VERSION@">proteomiqon-psmbasedquantification</requirement>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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10 </requirements>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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11 <command detect_errors="exit_code"><![CDATA[
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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12 #import re
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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13 #set instrumentOutput_basename = $re.sub(r'[^\w ,.\-+]','_',$instrumentOutput.element_identifier)
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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14 #set scoredPSMs_basename = $re.sub(r'[^\w ,.\-+]','_',$scoredPSMs.element_identifier)
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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15 #set peptideDB_basename = $re.sub(r'[^\w ,.\-+]','_',$peptideDB.element_identifier)
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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16 #if $outputParamfile:
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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17 cat '$paramfile' >> '$out_paramfile' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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18 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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19 ln -s '$instrumentOutput' '${instrumentOutput_basename}.mzlite' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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20 ln -s '$scoredPSMs' '${scoredPSMs_basename}.qpsm' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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21 ln -s '$peptideDB' '${peptideDB_basename}.db' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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22 ln -s '$out_quant' '${instrumentOutput_basename}.quant' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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23 proteomiqon-psmbasedquantification -i './${instrumentOutput_basename}.mzlite' -ii './${scoredPSMs_basename}.qpsm' -d './${peptideDB_basename}.db' -p '$paramfile' -o ./
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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24 ]]>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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25 </command>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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26 <configfiles>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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27 <configfile name="paramfile">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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28 <![CDATA[
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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29 {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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30 "PerformLabeledQuantification": ${PerformLabeledQuantification},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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31 "XicExtraction":
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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32 {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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33 "ScanTimeWindow": ${XicExtraction.ScanTimeWindow},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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34 "MzWindow_Da": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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35 "Case": "${XicExtraction.MzWindow_DaTypeCond.MzWindow_DaType}",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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36 #if $XicExtraction.MzWindow_DaTypeCond.MzWindow_DaType == "Fixed"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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37 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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38 ${XicExtraction.MzWindow_DaTypeCond.MzWindow_Da}
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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39 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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40 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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41 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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42 "XicProcessing": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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43 #if $XicExtraction.XicProcessing.ProcessingTypeCond.ProcessingType == "Wavelet"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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44 "Case": "Wavelet",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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45 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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46 {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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47 #if $XicExtraction.XicProcessing.ProcessingTypeCond.BorderPadding
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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48 "Borderpadding": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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49 "Case": "Some",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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50 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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51 ${XicExtraction.XicProcessing.ProcessingTypeCond.BorderPadding}
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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52 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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53 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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54 #else
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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55 "Borderpadding": null,
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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56 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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57 "BorderPadMethod": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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58 "Case": "${XicExtraction.XicProcessing.ProcessingTypeCond.BorderPadMethod}"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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59 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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60 "InternalPaddingMethod": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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61 "Case": "${XicExtraction.XicProcessing.ProcessingTypeCond.InternalPaddingMethod}"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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62 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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63 "HugeGapPaddingMethod": {
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64 "Case": "${XicExtraction.XicProcessing.ProcessingTypeCond.HugeGapPaddingMethod}"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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65 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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66 "HugeGapPaddingDistance": ${XicExtraction.XicProcessing.ProcessingTypeCond.HugeGapPaddingDistance},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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67 #if $XicExtraction.XicProcessing.ProcessingTypeCond.MinPeakDistance
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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68 "MinPeakDistance": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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69 "Case": "Some",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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70 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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71 ${XicExtraction.XicProcessing.ProcessingTypeCond.MinPeakDistance},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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72 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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73 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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74 #else
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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75 "MinPeakDistance": null,
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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76 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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77 #if $XicExtraction.XicProcessing.ProcessingTypeCond.MinPeakLength
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
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diff changeset
78 "MinPeakLength": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
79 "Case": "Some",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
80 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
81 ${XicExtraction.XicProcessing.ProcessingTypeCond.MinPeakLength}
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
82 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
83 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
84 #else
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
85 "MinPeakLength": null,
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
86 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
87 "MaxPeakLength": ${XicExtraction.XicProcessing.ProcessingTypeCond.MaxPeakLength},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
88 "NoiseQuantile": ${XicExtraction.XicProcessing.ProcessingTypeCond.NoiseQuantile},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
89 "MinSNR": ${XicExtraction.XicProcessing.ProcessingTypeCond.MinSNR},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
90 }
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
91 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
92 #else
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
93 "Case": "SecondDerivative",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
94 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
95 {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
96 "MinSNR": ${XicExtraction.XicProcessing.ProcessingTypeCond.MinSNR},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
97 "PolynomOrder": ${XicExtraction.XicProcessing.ProcessingTypeCond.PolynomOrder},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
98 "WindowSize": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
99 "Case": "${XicExtraction.XicProcessing.ProcessingTypeCond.WindowSizeCond.WindowSizeType}",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
100 "Fields" : [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
101 ${XicExtraction.XicProcessing.ProcessingTypeCond.WindowSizeCond.WindowSize}
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
102 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
103 }
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
104 }
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
105 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
106 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
107 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
108 #if $XicExtraction.TopKPSMs
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
109 "TopKPSMs": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
110 "Case": "Some",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
111 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
112 ${XicExtraction.TopKPSMs}
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
113 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
114 }
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
115 #else
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
116 "TopKPSMs": null
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
117 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
118 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
119 #if $BaseLineCorrectionCond.BaseLineCorrectionEnabled == "yes"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
120 "BaseLineCorrection": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
121 "Case": "Some",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
122 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
123 {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
124 "MaxIterations":$BaseLineCorrectionCond.MaxIterations,
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
125 "Lambda":$BaseLineCorrectionCond.Lambda,
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
126 "P":$BaseLineCorrectionCond.P
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
127 }
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
128 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
129 }
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
130 #else
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
131 "BaseLineCorrection": null
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
132 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
133 }
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
134 ]]>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
135 </configfile>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
136 </configfiles>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
137 <inputs>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
138 <param name="instrumentOutput" type="data" format="sqlite" label="Instrument output" help="Specify mass spectrometry data you want to analyze."/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
139 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM file" help="Specify list of peptide identifications."/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
140 <param name="peptideDB" type="data" format="sqlite" label="Peptide database" help="Specify the peptide data base."/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
141 <param name="PerformLabeledQuantification" type="boolean" checked="true" label="Perform labeled quantification" help="If checked, a quantification of peptides which contain an isotopic modification is performed. Additionally, for every identified peptide we check if the mass spectrometry run contains a peak at the m/z of the labeled/unlabeled counterpart and quantify it."/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
142 <section name="XicExtraction" title="XIC extraction">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
143 <param name="ScanTimeWindow" type="float" value="2.0" label="Scan timewindow" help="Specify the length of the scan time window used for XIC creation."/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
144 <conditional name="MzWindow_DaTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
145 <param name="MzWindow_DaType" type="select" label="MzWindow_Da type" help="Specify the MzWindow Da Type">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
146 <option value="Fixed" selected="true">Fixed</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
147 <option value="Estimate">Estimate</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
148 </param>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
149 <when value="Fixed">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
150 <param name="MzWindow_Da" type="float" value="0.07" label="Window width" help="Specify the m/z window set centered on the target m/z used for XIC creation" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
151 </when>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
152 <when value="Estimate">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
153 </when>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
154 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
155 <section name="XicProcessing" title="Xic processing">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
156 <conditional name="ProcessingTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
157 <param name="ProcessingType" type="select" label="Processing type">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
158 <option value="SecondDerivative">Second Derivative</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
159 <option value="Wavelet" selected="true">Wavelet</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
160 </param>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
161 <when value="SecondDerivative">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
162 <param name="MinSNR" type="float" value="2.0" label="Min SNR" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
163 <param name="PolynomOrder" type="integer" value="2" label="Polynom order" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
164 <conditional name="WindowSizeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
165 <param name="WindowSizeType" type="select" label="Window size type">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
166 <option value="Fixed" selected="true">Fixed</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
167 <option value="EstimateUsingAutoCorrelation">Estimate using auto correlation</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
168 </param>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
169 <when value="Fixed">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
170 <param name="WindowSize" type="integer" value="11" label="Value" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
171 </when>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
172 <when value="EstimateUsingAutoCorrelation">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
173 <param name="WindowSize" type="float" value="11.0" label="Value" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
174 </when>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
175 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
176 </when>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
177 <when value="Wavelet">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
178 <param name="BorderPadding" type="integer" value="2" optional="true" label="Border padding amount" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
179 <param name="BorderPadMethod" type="select" label="Border padding method">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
180 <option value="Random" selected="true">Random</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
181 <option value="Zero">Zero</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
182 </param>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
183 <param name="InternalPaddingMethod" type="select" label="Internal padding method">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
184 <option value="Random">Random</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
185 <option value="NaN">NaN</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
186 <option value="Delete">Delete</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
187 <option value="Zero">Zero</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
188 <option value="LinearInterpolation" selected="true">Linear Interpolation</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
189 </param>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
190 <param name="HugeGapPaddingMethod" type="select" label="Huge gap padding method">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
191 <option value="Random">Random</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
192 <option value="NaN">NaN</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
193 <option value="Delete">Delete</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
194 <option value="Zero" selected="true">Zero</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
195 <option value="LinearInterpolation">Linear Interpolation</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
196 </param>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
197 <param name="HugeGapPaddingDistance" type="float" value="100.0" label="Huge gap padding distance" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
198 <param name="MinPeakDistance" type="float" value="" optional="true" label="Min peak distance" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
199 <param name="MinPeakLength" type="float" value="0.1" optional="true" label="Min peak length" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
200 <param name="MaxPeakLength" type="float" value="1.5" label="Max peak length" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
201 <param name="NoiseQuantile" type="float" value="0.01" label="Noise quantile" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
202 <param name="MinSNR" type="float" value="0.01" label="Min SNR" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
203 </when>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
204 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
205 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
206 <param name="TopKPSMs" type="integer" value="3" optional="true" label="Top KPSMs" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
207 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
208 <conditional name="BaseLineCorrectionCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
209 <param name="BaseLineCorrectionEnabled" type="select" label="Use baseline correction">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
210 <option value="yes" selected="true">Yes</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
211 <option value="no">No</option>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
212 </param>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
213 <when value="yes">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
214 <param name="MaxIterations" type="integer" value="10" label="Max iterations" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
215 <param name="Lambda" type="integer" value="6" label="Lambda" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
216 <param name="P" type="float" value="0.05" label="P" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
217 </when>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
218 <when value="no">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
219 </when>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
220 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
221 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
222 </inputs>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
223 <outputs>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
224 <data format="tabular" name="out_quant" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
225 <data format="json" name="out_paramfile">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
226 <filter>outputParamfile</filter>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
227 </data>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
228 </outputs>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
229 <tests>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
230 <test expect_num_outputs="1">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
231 <param name="instrumentOutput" value="sample.mzlite"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
232 <param name="scoredPSMs" value="sample.qpsm"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
233 <param name="peptideDB" value="sample.db"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
234 <param name="PerformLabeledQuantification" value="true"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
235 <section name="XicExtraction">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
236 <param name="ScanTimeWindow" value="2.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
237 <section name="XicProcessing">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
238 <conditional name="ProcessingTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
239 <param name="ProcessingType" value="SecondDerivate" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
240 <param name="MinSNR" value="2.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
241 <param name="PolynomOrder" value="2"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
242 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
243 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
244 <conditional name="WindowSizeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
245 <param name="WindowSizeType" value="Fixed"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
246 <param name="WindowSize" value="11"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
247 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
248 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
249 <param name="TopKPSMs" value=""/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
250 <conditional name="BaseLineCorrectionCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
251 <param name="BaseLineCorrectionEnabled" value="yes"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
252 <param name="MaxIterations" value="10"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
253 <param name="Lambda" value="6"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
254 <param name="P" value="0.05"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
255 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
256 <param name="outputParamfile" value="false"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
257 </test>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
258 <test expect_num_outputs="2">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
259 <param name="instrumentOutput" value="sample.mzlite"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
260 <param name="scoredPSMs" value="sample.qpsm"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
261 <param name="peptideDB" value="sample.db"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
262 <param name="PerformLabeledQuantification" value="true"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
263 <section name="XicExtraction">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
264 <param name="ScanTimeWindow" value="2.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
265 <conditional name="MzWindow_DaTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
266 <param name="MzWindow_DaType" value="Fixed"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
267 <param name="MzWindow_Da" value="0.07"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
268 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
269 <section name="XicProcessing">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
270 <conditional name="ProcessingTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
271 <param name="ProcessingType" value="SecondDerivative" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
272 <param name="MinSNR" value="2.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
273 <param name="PolynomOrder" value="2"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
274 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
275 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
276 <conditional name="WindowSizeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
277 <param name="WindowSizeType" value="Fixed"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
278 <param name="WindowSize" value="11"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
279 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
280 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
281 <param name="TopKPSMs" value=""/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
282 <conditional name="BaseLineCorrectionCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
283 <param name="BaseLineCorrectionEnabled" value="yes"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
284 <param name="MaxIterations" value="10"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
285 <param name="Lambda" value="6"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
286 <param name="P" value="0.05"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
287 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
288 <param name="outputParamfile" value="true"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
289 <output name="out_paramfile" file="result_1.json" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
290 </test>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
291 <test expect_num_outputs="2">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
292 <param name="instrumentOutput" value="sample.mzlite"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
293 <param name="scoredPSMs" value="sample.qpsm"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
294 <param name="peptideDB" value="sample.db"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
295 <param name="PerformLabeledQuantification" value="true"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
296 <section name="XicExtraction">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
297 <param name="ScanTimeWindow" value="2.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
298 <conditional name="MzWindow_DaTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
299 <param name="MzWindow_DaType" value="Estimate"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
300 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
301 <section name="XicProcessing">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
302 <conditional name="ProcessingTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
303 <param name="ProcessingType" value="Wavelet" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
304 <param name="BorderPadding" value="2"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
305 <param name="BorderPadMethod" value="Random" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
306 <param name="InternalPaddingMethod" value="LinearInterpolation"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
307 <param name="HugeGapPaddingMethod" value="Zero"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
308 <param name="HugeGapPaddingDistance" value="100.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
309 <param name="MinPeakDistance" value=""/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
310 <param name="MinPeakLength" value="0.1"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
311 <param name="MaxPeakLength" value="1.5"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
312 <param name="NoiseQuantile" value="0.01"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
313 <param name="MinSNR" value="0.01" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
314 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
315 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
316 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
317 <param name="TopKPSMs" value="3"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
318 <conditional name="BaseLineCorrectionCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
319 <param name="BaseLineCorrectionEnabled" value="no"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
320 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
321 <param name="outputParamfile" value="true"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
322 <output name="out_paramfile" file="result_2.json" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
323 </test>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
324 <test expect_num_outputs="2">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
325 <param name="instrumentOutput" value="sample.mzlite"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
326 <param name="scoredPSMs" value="sample.qpsm"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
327 <param name="peptideDB" value="sample.db"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
328 <param name="PerformLabeledQuantification" value="true"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
329 <section name="XicExtraction">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
330 <param name="ScanTimeWindow" value="2.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
331 <conditional name="MzWindow_DaTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
332 <param name="MzWindow_DaType" value="Estimate"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
333 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
334 <section name="XicProcessing">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
335 <conditional name="ProcessingTypeCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
336 <param name="ProcessingType" value="Wavelet" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
337 <param name="BorderPadding" value=""/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
338 <param name="BorderPadMethod" value="Zero" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
339 <param name="InternalPaddingMethod" value="Zero"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
340 <param name="HugeGapPaddingMethod" value="Delete"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
341 <param name="HugeGapPaddingDistance" value="101.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
342 <param name="MinPeakDistance" value="2.0"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
343 <param name="MinPeakLength" value=""/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
344 <param name="MaxPeakLength" value="1.5"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
345 <param name="NoiseQuantile" value="0.01"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
346 <param name="MinSNR" value="0.01" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
347 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
348 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
349 </section>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
350 <param name="TopKPSMs" value=""/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
351 <conditional name="BaseLineCorrectionCond">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
352 <param name="BaseLineCorrectionEnabled" value="no"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
353 </conditional>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
354 <param name="outputParamfile" value="true"/>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
355 <output name="out_paramfile" file="result_3.json" />
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
356 </test>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
357 </tests>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
358 <help>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
359 <![CDATA[
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
360 What It Does
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
361 ------------
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
362 **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>`_ which `passed fdr thresholds <https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html>`_.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
363
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
364 Once a MS/MS spectrum is mapped to a peptide sequence the quantity of the fragmented peptide ion comes into view.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
365
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
366 Given an MS run in the mzLite or mzml format and a list of fdr controlled peptide spectrum matches, this tool iterates accross all identified MS/MS scans and groups them by the assigned peptide ion.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
367 The scan times of each MS/MS spectrum are then weighted according to the quality of each match to build an reliable estimator for the scan time of the peptide ion in question.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
368 This scan time estimator, combined with the monoisotopic m/z, is then used to extract an ion chromatogram.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
369 Using wavelet based peak detection techniques we identify all peaks present in the XIC and select the most probable peak our target for quantification.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
370 Using parameter estimation techniques we subsequently use peak fitting to fit a set of two gaussian models to the detected peak, from whom the one with the better fit is selected.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
371 This allows us not only to report how well the signal fitted to the theoretical expected peak shape but also to obtain accurate estimates for the peak area, our estimator for peptide ion abundance.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
372
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
373 .. image:: LabeledQuant.png
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
374 :width: 768pt
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
375 :height: 228pt
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
376
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
377 The quantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
378 For this we use the known identity of one of the the peptide ions and calculate the m/z of the unobserved differentially labeled counterpart to extract and quantify the corresponding XIC.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
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diff changeset
379
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
380 Further Reading
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
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diff changeset
381 ---------------
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
382 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html>`_.
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
383 ]]>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
parents:
diff changeset
384 </help>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152"
galaxyp
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diff changeset
385 </tool>