proteomiqon_psmbasedquantification: proteomiqon_psmbasedquantification.xml annotate

annotate proteomiqon_psmbasedquantification.xml @ 1:4abcc674fc0b draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 08e65e1c3975aa0a08a840f06f4118bf145308c0"

author	galaxyp
date	Fri, 29 Apr 2022 09:10:15 +0000
parents	65ce27f0fa01
children

rev	line source
0 65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	2 <description>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	4 </description>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	5 <macros>
1 4abcc674fc0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 08e65e1c3975aa0a08a840f06f4118bf145308c0" galaxyp parents: 0 diff changeset	6 <token name="@VERSION@">0.0.8</token>
0 65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	7 </macros>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	8 <requirements>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	10 </requirements>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	12 #import re
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	16 #if $outputParamfile:
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	17 cat '$paramfile' >> '$out_paramfile' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	18 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	19 ln -s '$instrumentOutput' '${instrumentOutput_basename}.mzlite' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	20 ln -s '$scoredPSMs' '${scoredPSMs_basename}.qpsm' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	21 ln -s '$peptideDB' '${peptideDB_basename}.db' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	22 ln -s '$out_quant' '${instrumentOutput_basename}.quant' &&
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	23 proteomiqon-psmbasedquantification -i './${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" galaxyp parents: diff changeset	24 ]]>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	25 </command>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	26 <configfiles>
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	27 <configfile name="paramfile">
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	28 <![CDATA[
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	29 {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	30 "PerformLabeledQuantification": ${PerformLabeledQuantification},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	31 "XicExtraction":
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	32 {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	33 "ScanTimeWindow": ${XicExtraction.ScanTimeWindow},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	34 "MzWindow_Da": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	35 "Case": "${XicExtraction.MzWindow_DaTypeCond.MzWindow_DaType}",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	37 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	38 ${XicExtraction.MzWindow_DaTypeCond.MzWindow_Da}
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	39 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	40 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	41 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	42 "XicProcessing": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	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" galaxyp parents: diff changeset	44 "Case": "Wavelet",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	45 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	46 {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	47 #if $XicExtraction.XicProcessing.ProcessingTypeCond.BorderPadding
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	48 "Borderpadding": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	49 "Case": "Some",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	50 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	51 ${XicExtraction.XicProcessing.ProcessingTypeCond.BorderPadding}
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	52 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	53 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	54 #else
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	55 "Borderpadding": null,
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	56 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	57 "BorderPadMethod": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	58 "Case": "${XicExtraction.XicProcessing.ProcessingTypeCond.BorderPadMethod}"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	59 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	60 "InternalPaddingMethod": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	61 "Case": "${XicExtraction.XicProcessing.ProcessingTypeCond.InternalPaddingMethod}"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	62 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	63 "HugeGapPaddingMethod": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	64 "Case": "${XicExtraction.XicProcessing.ProcessingTypeCond.HugeGapPaddingMethod}"
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	65 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	66 "HugeGapPaddingDistance": ${XicExtraction.XicProcessing.ProcessingTypeCond.HugeGapPaddingDistance},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	67 #if $XicExtraction.XicProcessing.ProcessingTypeCond.MinPeakDistance
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	68 "MinPeakDistance": {
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	69 "Case": "Some",
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	70 "Fields": [
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	71 ${XicExtraction.XicProcessing.ProcessingTypeCond.MinPeakDistance},
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	72 ]
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	73 },
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	74 #else
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	75 "MinPeakDistance": null,
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	76 #end if
65ce27f0fa01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" galaxyp parents: diff changeset	77 #if $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	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 parents: 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 parents: 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 parents: diff changeset	385 </tool>

Mercurial > repos > galaxyp > proteomiqon_psmbasedquantification

annotate proteomiqon_psmbasedquantification.xml @ 1:4abcc674fc0b draft default tip