Mercurial > repos > galaxyp > proteomiqon_labeledproteinquantification
diff labeledproteinquantification.xml @ 0:cbdfdca98db3 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification commit eda2d62c81b38ed3975482d0198e3dd75ff1d74f"
| author | galaxyp |
|---|---|
| date | Thu, 16 Sep 2021 21:11:34 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/labeledproteinquantification.xml Thu Sep 16 21:11:34 2021 +0000 @@ -0,0 +1,2527 @@ +<tool id="proteomiqon_labeledproteinquantification" name="Proteomiqon LabeledProteinQuantification" version="@VERSION@" profile="20.05"> + <description> + estimates protein abundances using quantified peptide ions. + </description> + <macros> + <token name="@VERSION@">0.0.1</token> + <import>aggregationparams.xml</import> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">proteomiqon-labeledproteinquantification</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #import re + #for $quantAndProtFile in $proteinassignedquantpepions + #set basename = $re.sub(r'[^\w ,.\-+]','_',$quantAndProtFile.element_identifier) + ln -s '$quantAndProtFile' '${basename}.quantAndProt' && + #end for + #if $outputParamfile: + cat '$paramfile' >> '$out_paramfile' && + #end if + ln -s '$out_labeledQuant' 'LabeledQuant.txt' && + proteomiqon-labeledproteinquantification -i './' -p '$paramfile' -o './' + ]]> + </command> + <configfiles> + <configfile name="paramfile"> + <![CDATA[ + { + #if $CorrelationLightHeavyThreshold + "Correlation_Light_Heavy_Threshold": { + "Case": "Some", + "Fields": [ + ${CorrelationLightHeavyThreshold} + ] + }, + #else + "Correlation_Light_Heavy_Threshold": null, + #end if + "ModificationFilter": { + "Case": "${ModificationFilterCond.ModificationFilter}", + #if $ModificationFilterCond.ModificationFilter == "UseOnly" + "Fields": [ + [ + #for $mod in $ModificationFilterCond.ModificationFilterSequence + { + "Case": "${mod}" + }, + #end for + ] + ] + #end if + }, + "AggregateGlobalModificationsParams": { + #set $aggregationParams = $GlobalAggregationParams + #set $labeledTransformSection = $aggregationParams.LabeledTransform + #set $labeledTransformLight = $labeledTransformSection.LabeledTransformLightCond + #set $labeledTransformHeavy = $labeledTransformSection.LabeledTransformHeavyCond + #set $labeledTransformRatio = $labeledTransformSection.LabeledTransformRatioCond + #if $labeledTransformLight.Type == "None" and $labeledTransformHeavy.Type == "None" and $labeledTransformRatio.Type == "None" + "LabeledTransform": null, + #else + "LabeledTransform": { + "Case": "Some", + "Fields": [ + { + #if $labeledTransformLight.Type == "None" + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformLight.Type}", + #if $labeledTransformLight.Type != "Log2" + "Fields": [ + $labeledTransformLight.Value + ] + #end if + } + ] + }, + #end if + #if $labeledTransformHeavy.Type == "None" + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformHeavy.Type}", + #if $labeledTransformHeavy.Type != "Log2" + "Fields": [ + $labeledTransformHeavy.Value + ] + #end if + } + ] + }, + #end if + #if $labeledTransformRatio.Type == "None" + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformRatio.Type}", + #if $labeledTransformRatio.Type != "Log2" + "Fields": [ + $labeledTransformRatio.Value + ] + #end if + } + ] + } + #end if + } + ] + }, + #end if + #set $labeledSingleFiltersSection = $aggregationParams.LabeledSingleFilters + #set $labeledSingleFiltersLight = $labeledSingleFiltersSection.Light + #set $labeledSingleFiltersHeavy = $labeledSingleFiltersSection.Heavy + #set $labeledSingleFiltersRatio = $labeledSingleFiltersSection.Ratio + #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan and \ + not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan and \ + not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan + "LabeledSingleFilters": null, + #else + "LabeledSingleFilters": { + "Case": "Some", + "Fields": [ + { + #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersLight.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersLight.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersLight.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersLight.SmallerThan + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersHeavy.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersHeavy.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersHeavy.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersHeavy.SmallerThan + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersRatio.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersRatio.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersRatio.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersRatio.SmallerThan + ] + } + #end if + ] + ] + } + #end if + } + ] + }, + #end if + #set $labeledGroupFiltersSection = $aggregationParams.LabeledGroupFilters + #set $labeledGroupFiltersLight = $labeledGroupFiltersSection.Light + #set $labeledGroupFiltersHeavy = $labeledGroupFiltersSection.Heavy + #set $labeledGroupFiltersRatio = $labeledGroupFiltersSection.Ratio + #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev and \ + not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev and \ + not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev + "LabeledGroupFilters": null, + #else + "LabeledGroupFilters": { + "Case": "Some", + "Fields": [ + { + + + #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersLight.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersLight.Tukey + ] + }, + #end if + #if $labeledGroupFiltersLight.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersLight.Stdev + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersHeavy.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersHeavy.Tukey + ] + }, + #end if + #if $labeledGroupFiltersHeavy.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersHeavy.Stdev + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersRatio.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersRatio.Tukey + ] + }, + #end if + #if $labeledGroupFiltersRatio.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersRatio.Stdev + ] + } + #end if + ] + ] + } + #end if + } + ] + }, + #end if + "LabeledAggregation": { + "Light": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationLight}" + }, + "Heavy": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationHeavy}" + }, + "Ratio": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationRatio}" + } + } + }, + #set $aggregationParams = $AggregatePeptideChargeStatesParams.AggregatePeptideChargeStatesParamsCond + #if $aggregationParams.AggregatePeptideChargeStatesParamsEnabled == "no" + "AggregatePeptideChargeStatesParams": null, + #else + "AggregatePeptideChargeStatesParams": { + "Case": "Some", + "Fields": [ + { + #set $labeledTransformSection = $aggregationParams.LabeledTransform + #set $labeledTransformLight = $labeledTransformSection.LabeledTransformLightCond + #set $labeledTransformHeavy = $labeledTransformSection.LabeledTransformHeavyCond + #set $labeledTransformRatio = $labeledTransformSection.LabeledTransformRatioCond + #if $labeledTransformLight.Type == "None" and $labeledTransformHeavy.Type == "None" and $labeledTransformRatio.Type == "None" + "LabeledTransform": null, + #else + "LabeledTransform": { + "Case": "Some", + "Fields": [ + { + #if $labeledTransformLight.Type == "None" + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformLight.Type}", + #if $labeledTransformLight.Type != "Log2" + "Fields": [ + $labeledTransformLight.Value + ] + #end if + } + ] + }, + #end if + #if $labeledTransformHeavy.Type == "None" + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformHeavy.Type}", + #if $labeledTransformHeavy.Type != "Log2" + "Fields": [ + $labeledTransformHeavy.Value + ] + #end if + } + ] + }, + #end if + #if $labeledTransformRatio.Type == "None" + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformRatio.Type}", + #if $labeledTransformRatio.Type != "Log2" + "Fields": [ + $labeledTransformRatio.Value + ] + #end if + } + ] + } + #end if + } + ] + }, + #end if + #set $labeledSingleFiltersSection = $aggregationParams.LabeledSingleFilters + #set $labeledSingleFiltersLight = $labeledSingleFiltersSection.Light + #set $labeledSingleFiltersHeavy = $labeledSingleFiltersSection.Heavy + #set $labeledSingleFiltersRatio = $labeledSingleFiltersSection.Ratio + #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan and \ + not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan and \ + not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan + "LabeledSingleFilters": null, + #else + "LabeledSingleFilters": { + "Case": "Some", + "Fields": [ + { + #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersLight.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersLight.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersLight.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersLight.SmallerThan + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersHeavy.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersHeavy.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersHeavy.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersHeavy.SmallerThan + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersRatio.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersRatio.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersRatio.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersRatio.SmallerThan + ] + } + #end if + ] + ] + } + #end if + } + ] + }, + #end if + #set $labeledGroupFiltersSection = $aggregationParams.LabeledGroupFilters + #set $labeledGroupFiltersLight = $labeledGroupFiltersSection.Light + #set $labeledGroupFiltersHeavy = $labeledGroupFiltersSection.Heavy + #set $labeledGroupFiltersRatio = $labeledGroupFiltersSection.Ratio + #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev and \ + not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev and \ + not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev + "LabeledGroupFilters": null, + #else + "LabeledGroupFilters": { + "Case": "Some", + "Fields": [ + { + #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersLight.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersLight.Tukey + ] + }, + #end if + #if $labeledGroupFiltersLight.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersLight.Stdev + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersHeavy.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersHeavy.Tukey + ] + }, + #end if + #if $labeledGroupFiltersHeavy.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersHeavy.Stdev + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersRatio.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersRatio.Tukey + ] + }, + #end if + #if $labeledGroupFiltersRatio.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersRatio.Stdev + ] + } + #end if + ] + ] + } + #end if + } + ] + }, + #end if + "LabeledAggregation": { + "Light": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationLight}" + }, + "Heavy": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationHeavy}" + }, + "Ratio": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationRatio}" + } + } + } + ] + }, + #end if + #set $aggregationParams = $AggregateModifiedPeptidesParams.AggregateModifiedPeptidesParamsCond + #if $aggregationParams.AggregateModifiedPeptidesParamsEnabled == "no" + "AggregateModifiedPeptidesParams": null, + #else + "AggregateModifiedPeptidesParams": { + "Case": "Some", + "Fields": [ + { + #set $labeledTransformSection = $aggregationParams.LabeledTransform + #set $labeledTransformLight = $labeledTransformSection.LabeledTransformLightCond + #set $labeledTransformHeavy = $labeledTransformSection.LabeledTransformHeavyCond + #set $labeledTransformRatio = $labeledTransformSection.LabeledTransformRatioCond + #if $labeledTransformLight.Type == "None" and $labeledTransformHeavy.Type == "None" and $labeledTransformRatio.Type == "None" + "LabeledTransform": null, + #else + "LabeledTransform": { + "Case": "Some", + "Fields": [ + { + #if $labeledTransformLight.Type == "None" + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformLight.Type}", + #if $labeledTransformLight.Type != "Log2" + "Fields": [ + $labeledTransformLight.Value + ] + #end if + } + ] + }, + #end if + #if $labeledTransformHeavy.Type == "None" + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformHeavy.Type}", + #if $labeledTransformHeavy.Type != "Log2" + "Fields": [ + $labeledTransformHeavy.Value + ] + #end if + } + ] + }, + #end if + #if $labeledTransformRatio.Type == "None" + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformRatio.Type}", + #if $labeledTransformRatio.Type != "Log2" + "Fields": [ + $labeledTransformRatio.Value + ] + #end if + } + ] + } + #end if + } + ] + }, + #end if + #set $labeledSingleFiltersSection = $aggregationParams.LabeledSingleFilters + #set $labeledSingleFiltersLight = $labeledSingleFiltersSection.Light + #set $labeledSingleFiltersHeavy = $labeledSingleFiltersSection.Heavy + #set $labeledSingleFiltersRatio = $labeledSingleFiltersSection.Ratio + #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan and \ + not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan and \ + not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan + "LabeledSingleFilters": null, + #else + "LabeledSingleFilters": { + "Case": "Some", + "Fields": [ + { + #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersLight.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersLight.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersLight.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersLight.SmallerThan + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersHeavy.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersHeavy.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersHeavy.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersHeavy.SmallerThan + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersRatio.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersRatio.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersRatio.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersRatio.SmallerThan + ] + } + #end if + ] + ] + } + #end if + } + ] + }, + #end if + #set $labeledGroupFiltersSection = $aggregationParams.LabeledGroupFilters + #set $labeledGroupFiltersLight = $labeledGroupFiltersSection.Light + #set $labeledGroupFiltersHeavy = $labeledGroupFiltersSection.Heavy + #set $labeledGroupFiltersRatio = $labeledGroupFiltersSection.Ratio + #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev and \ + not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev and \ + not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev + "LabeledGroupFilters": null, + #else + "LabeledGroupFilters": { + "Case": "Some", + "Fields": [ + { + #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersLight.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersLight.Tukey + ] + }, + #end if + #if $labeledGroupFiltersLight.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersLight.Stdev + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersHeavy.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersHeavy.Tukey + ] + }, + #end if + #if $labeledGroupFiltersHeavy.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersHeavy.Stdev + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersRatio.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersRatio.Tukey + ] + }, + #end if + #if $labeledGroupFiltersRatio.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersRatio.Stdev + ] + } + #end if + ] + ] + } + #end if + } + ] + }, + #end if + "LabeledAggregation": { + "Light": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationLight}" + }, + "Heavy": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationHeavy}" + }, + "Ratio": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationRatio}" + } + } + } + ] + }, + #end if + "AggregateToProteinGroupsParams": { + #set $aggregationParams = $AggregateToProteinGroupsParams + #set $labeledTransformSection = $aggregationParams.LabeledTransform + #set $labeledTransformLight = $labeledTransformSection.LabeledTransformLightCond + #set $labeledTransformHeavy = $labeledTransformSection.LabeledTransformHeavyCond + #set $labeledTransformRatio = $labeledTransformSection.LabeledTransformRatioCond + #if $labeledTransformLight.Type == "None" and $labeledTransformHeavy.Type == "None" and $labeledTransformRatio.Type == "None" + "LabeledTransform": null, + #else + "LabeledTransform": { + "Case": "Some", + "Fields": [ + { + #if $labeledTransformLight.Type == "None" + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformLight.Type}", + #if $labeledTransformLight.Type != "Log2" + "Fields": [ + $labeledTransformLight.Value + ] + #end if + } + ] + }, + #end if + #if $labeledTransformHeavy.Type == "None" + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformHeavy.Type}", + #if $labeledTransformHeavy.Type != "Log2" + "Fields": [ + $labeledTransformHeavy.Value + ] + #end if + } + ] + }, + #end if + #if $labeledTransformRatio.Type == "None" + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + { + "Case": "${labeledTransformRatio.Type}", + #if $labeledTransformRatio.Type != "Log2" + "Fields": [ + $labeledTransformRatio.Value + ] + #end if + } + ] + } + #end if + } + ] + }, + #end if + #set $labeledSingleFiltersSection = $aggregationParams.LabeledSingleFilters + #set $labeledSingleFiltersLight = $labeledSingleFiltersSection.Light + #set $labeledSingleFiltersHeavy = $labeledSingleFiltersSection.Heavy + #set $labeledSingleFiltersRatio = $labeledSingleFiltersSection.Ratio + #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan and \ + not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan and \ + not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan + "LabeledSingleFilters": null, + #else + "LabeledSingleFilters": { + "Case": "Some", + "Fields": [ + { + #if not $labeledSingleFiltersLight.BiggerThan and not $labeledSingleFiltersLight.SmallerThan + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersLight.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersLight.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersLight.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersLight.SmallerThan + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledSingleFiltersHeavy.BiggerThan and not $labeledSingleFiltersHeavy.SmallerThan + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersHeavy.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersHeavy.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersHeavy.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersHeavy.SmallerThan + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledSingleFiltersRatio.BiggerThan and not $labeledSingleFiltersRatio.SmallerThan + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + [ + #if $labeledSingleFiltersRatio.BiggerThan + { + "Case": "IsBiggerThan", + "Fields": [ + $labeledSingleFiltersRatio.BiggerThan + ] + }, + #end if + #if $labeledSingleFiltersRatio.SmallerThan + { + "Case": "IsSmallerThan", + "Fields": [ + $labeledSingleFiltersRatio.SmallerThan + ] + } + #end if + ] + ] + } + #end if + } + ] + }, + #end if + #set $labeledGroupFiltersSection = $aggregationParams.LabeledGroupFilters + #set $labeledGroupFiltersLight = $labeledGroupFiltersSection.Light + #set $labeledGroupFiltersHeavy = $labeledGroupFiltersSection.Heavy + #set $labeledGroupFiltersRatio = $labeledGroupFiltersSection.Ratio + #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev and \ + not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev and \ + not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev + "LabeledGroupFilters": null, + #else + "LabeledGroupFilters": { + "Case": "Some", + "Fields": [ + { + #if not $labeledGroupFiltersLight.Tukey and not $labeledGroupFiltersLight.Stdev + "Light": null, + #else + "Light": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersLight.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersLight.Tukey + ] + }, + #end if + #if $labeledGroupFiltersLight.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersLight.Stdev + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledGroupFiltersHeavy.Tukey and not $labeledGroupFiltersHeavy.Stdev + "Heavy": null, + #else + "Heavy": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersHeavy.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersHeavy.Tukey + ] + }, + #end if + #if $labeledGroupFiltersHeavy.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersHeavy.Stdev + ] + } + #end if + ] + ] + }, + #end if + #if not $labeledGroupFiltersRatio.Tukey and not $labeledGroupFiltersRatio.Stdev + "Ratio": null + #else + "Ratio": { + "Case": "Some", + "Fields": [ + [ + #if $labeledGroupFiltersRatio.Tukey + { + "Case": "Tukey", + "Fields": [ + $labeledGroupFiltersRatio.Tukey + ] + }, + #end if + #if $labeledGroupFiltersRatio.Stdev + { + "Case": "Stdev", + "Fields": [ + $labeledGroupFiltersRatio.Stdev + ] + } + #end if + ] + ] + } + #end if + } + ] + }, + #end if + "LabeledAggregation": { + "Light": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationLight}" + }, + "Heavy": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationHeavy}" + }, + "Ratio": { + "Case": "${aggregationParams.LabeledAggregation.labeledAggregationRatio}" + } + } + } + } + ]]> + </configfile> + </configfiles> + <inputs> + <param name="proteinassignedquantpepions" type="data" format="tabular" label="Protein assigned quant pep ions" help="Specify list of .quantAndProt files" multiple="true"/> + <param name="CorrelationLightHeavyThreshold" type="float" value="0.0" optional="true" label="Correlation Light Heavy Threshold" /> + <conditional name="ModificationFilterCond"> + <param name="ModificationFilter" type="select" label="Modification Filter"> + <option value="All" selected="true">All</option> + <option value="No">No</option> + <option value="UseOnly">Use Only</option> + </param> + <when value="All"> + </when> + <when value="No"> + </when> + <when value="UseOnly"> + <param name="ModificationFilterSequence" type="select" label="Sequence" multiple="true"> + <option value="Acetylation'ProtNTerm'">Acetylation'ProtNTerm'</option> + <option value="Carbamidomethyl'Cys'">Carbamidomethyl'Cys'</option> + <option value="Oxidation'Met'">Oxidation'Met'</option> + <option value="Phosphorylation'Ser'Thr'Tyr'">Phosphorylation'Ser'Thr'Tyr'</option> + <option value="Pyro_Glu'GluNterm'">Pyro_Glu'GluNterm'</option> + <option value="Pyro_Glu'GlnNterm'">Pyro_Glu'GlnNterm'</option> + </param> + </when> + </conditional> + <section name="GlobalAggregationParams" title="Aggregate Global Modifications Parameters"> + <expand macro="AggregationParams" /> + </section> + <section name="AggregatePeptideChargeStatesParams" title="Aggregate Peptide Charge States Parameters"> + <conditional name="AggregatePeptideChargeStatesParamsCond"> + <param name="AggregatePeptideChargeStatesParamsEnabled" type="select" label="Specify Aggregate Peptide Charge States Parameters?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <expand macro="AggregationParams" /> + </when> + <when value="no"> + </when> + </conditional> + </section> + <section name="AggregateModifiedPeptidesParams" title="Aggregate Modified Peptides Parameters"> + <conditional name="AggregateModifiedPeptidesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" type="select" label="Specify Aggregate Modified Peptides Parameters?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <expand macro="AggregationParams" /> + </when> + <when value="no"> + </when> + </conditional> + </section> + <section name="AggregateToProteinGroupsParams" title="Aggregate To Protein Groups Parameters"> + <expand macro="AggregationParams" /> + </section> + <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/> + </inputs> + <outputs> + <data format="tabular" name="out_labeledQuant" /> + <data format="json" name="out_paramfile"> + <filter>outputParamfile</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> + <param name="CorrelationLightHeavyThreshold" value="0.0"/> + <conditional name="ModificationFilterCond"> + <param name="ModificationFilter" value="All"/> + </conditional> + <section name="GlobalAggregationParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="None"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="None"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="None"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + <section name="Heavy"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + <section name="Ratio"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Mean"/> + <param name="labeledAggregationHeavy" value="Mean"/> + <param name="labeledAggregationRatio" value="Mean"/> + </section> + </section> + <section name="AggregatePeptideChargeStatesParams"> + <conditional name="AggregatePeptideChargeStatesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="no" /> + </conditional> + </section> + <section name="AggregateModifiedPeptidesParams"> + <conditional name="AggregateModifiedPeptidesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="no"/> + </conditional> + </section> + <section name="AggregateToProteinGroupsParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="None"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="None"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="None"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + <section name="Heavy"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + <section name="Ratio"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Mean"/> + <param name="labeledAggregationHeavy" value="Mean"/> + <param name="labeledAggregationRatio" value="Mean"/> + </section> + </section> + <param name="outputParamfile" value="false"/> + </test> + <test expect_num_outputs="2"> + <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> + <param name="CorrelationLightHeavyThreshold" value="0.0"/> + <conditional name="ModificationFilterCond"> + <param name="ModificationFilter" value="All"/> + </conditional> + <section name="GlobalAggregationParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="None"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="None"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="None"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + <section name="Heavy"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + <section name="Ratio"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Mean"/> + <param name="labeledAggregationHeavy" value="Mean"/> + <param name="labeledAggregationRatio" value="Mean"/> + </section> + </section> + <section name="AggregatePeptideChargeStatesParams"> + <conditional name="AggregatePeptideChargeStatesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="no" /> + </conditional> + </section> + <section name="AggregateModifiedPeptidesParams"> + <conditional name="AggregateModifiedPeptidesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="no"/> + </conditional> + </section> + <section name="AggregateToProteinGroupsParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="None"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="None"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="None"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + <section name="Heavy"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + <section name="Ratio"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Mean"/> + <param name="labeledAggregationHeavy" value="Mean"/> + <param name="labeledAggregationRatio" value="Mean"/> + </section> + </section> + <param name="outputParamfile" value="true"/> + <output name="out_paramfile" file="result_1.json"/> + </test> + <test expect_num_outputs="2"> + <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> + <param name="CorrelationLightHeavyThreshold" value="1.0"/> + <conditional name="ModificationFilterCond"> + <param name="ModificationFilter" value="No"/> + </conditional> + <section name="GlobalAggregationParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="Log2"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </section> + <section name="AggregatePeptideChargeStatesParams"> + <conditional name="AggregatePeptideChargeStatesParamsCond"> + <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="Log2"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </conditional> + </section> + <section name="AggregateModifiedPeptidesParams"> + <conditional name="AggregateModifiedPeptidesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="Log2"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </conditional> + </section> + <section name="AggregateToProteinGroupsParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="Log2"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </section> + <param name="outputParamfile" value="true"/> + <output name="out_paramfile" file="result_2.json"/> + </test> + <test expect_num_outputs="2"> + <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> + <param name="CorrelationLightHeavyThreshold" value="1.0"/> + <conditional name="ModificationFilterCond"> + <param name="ModificationFilter" value="No"/> + </conditional> + <section name="GlobalAggregationParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </section> + <section name="AggregatePeptideChargeStatesParams"> + <conditional name="AggregatePeptideChargeStatesParamsCond"> + <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="Log2"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </conditional> + </section> + <section name="AggregateModifiedPeptidesParams"> + <conditional name="AggregateModifiedPeptidesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="Log2"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </conditional> + </section> + <section name="AggregateToProteinGroupsParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Log2"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="Log2"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value=""/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value=""/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </section> + <param name="outputParamfile" value="true"/> + <output name="out_paramfile" file="result_3.json"/> + </test> + <test expect_num_outputs="2"> + <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> + <param name="CorrelationLightHeavyThreshold" value="1.0"/> + <conditional name="ModificationFilterCond"> + <param name="ModificationFilter" value="No"/> + </conditional> + <section name="GlobalAggregationParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </section> + <section name="AggregatePeptideChargeStatesParams"> + <conditional name="AggregatePeptideChargeStatesParamsCond"> + <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </conditional> + </section> + <section name="AggregateModifiedPeptidesParams"> + <conditional name="AggregateModifiedPeptidesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </conditional> + </section> + <section name="AggregateToProteinGroupsParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value=""/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value=""/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Median"/> + <param name="labeledAggregationHeavy" value="Sum"/> + <param name="labeledAggregationRatio" value="Sum"/> + </section> + </section> + <param name="outputParamfile" value="true"/> + <output name="out_paramfile" file="result_4.json"/> + </test> + <test expect_num_outputs="2"> + <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> + <param name="CorrelationLightHeavyThreshold" value="1.0"/> + <conditional name="ModificationFilterCond"> + <param name="ModificationFilter" value="No"/> + </conditional> + <section name="GlobalAggregationParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Sum"/> + <param name="labeledAggregationHeavy" value="Median"/> + <param name="labeledAggregationRatio" value="Median"/> + </section> + </section> + <section name="AggregatePeptideChargeStatesParams"> + <conditional name="AggregatePeptideChargeStatesParamsCond"> + <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Sum"/> + <param name="labeledAggregationHeavy" value="Median"/> + <param name="labeledAggregationRatio" value="Median"/> + </section> + </conditional> + </section> + <section name="AggregateModifiedPeptidesParams"> + <conditional name="AggregateModifiedPeptidesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Sum"/> + <param name="labeledAggregationHeavy" value="Median"/> + <param name="labeledAggregationRatio" value="Median"/> + </section> + </conditional> + </section> + <section name="AggregateToProteinGroupsParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value=""/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value=""/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Sum"/> + <param name="labeledAggregationHeavy" value="Median"/> + <param name="labeledAggregationRatio" value="Median"/> + </section> + </section> + <param name="outputParamfile" value="true"/> + <output name="out_paramfile" file="result_5.json"/> + </test> + <test expect_num_outputs="2"> + <param name="proteinassignedquantpepions" value="sample.quantAndProt"/> + <param name="CorrelationLightHeavyThreshold" value="1.0"/> + <conditional name="ModificationFilterCond"> + <param name="ModificationFilter" value="UseOnly"/> + <param name="ModificationFilterSequence" value="Acetylation'ProtNTerm',Carbamidomethyl'Cys',Oxidation'Met',Phosphorylation'Ser'Thr'Tyr',Pyro_Glu'GluNterm',Pyro_Glu'GlnNterm'"/> + </conditional> + <section name="GlobalAggregationParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Sum"/> + <param name="labeledAggregationHeavy" value="Median"/> + <param name="labeledAggregationRatio" value="Median"/> + </section> + </section> + <section name="AggregatePeptideChargeStatesParams"> + <conditional name="AggregatePeptideChargeStatesParamsCond"> + <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" /> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Sum"/> + <param name="labeledAggregationHeavy" value="Median"/> + <param name="labeledAggregationRatio" value="Median"/> + </section> + </conditional> + </section> + <section name="AggregateModifiedPeptidesParams"> + <conditional name="AggregateModifiedPeptidesParamsCond"> + <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Sum"/> + <param name="labeledAggregationHeavy" value="Median"/> + <param name="labeledAggregationRatio" value="Median"/> + </section> + </conditional> + </section> + <section name="AggregateToProteinGroupsParams"> + <section name="LabeledTransform"> + <conditional name="LabeledTransformLightCond"> + <param name="Type" value="Substract"/> + <param name="Value" value="2"/> + </conditional> + <conditional name="LabeledTransformHeavyCond"> + <param name="Type" value="Add"/> + <param name="Value" value="3"/> + </conditional> + <conditional name="LabeledTransformRatioCond"> + <param name="Type" value="DivideBy"/> + <param name="Value" value="4"/> + </conditional> + </section> + <section name="LabeledSingleFilters"> + <section name="Light"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value="2"/> + </section> + <section name="Heavy"> + <param name="BiggerThan" value="1"/> + <param name="SmallerThan" value=""/> + </section> + <section name="Ratio"> + <param name="BiggerThan" value=""/> + <param name="SmallerThan" value=""/> + </section> + </section> + <section name="LabeledGroupFilters"> + <section name="Light"> + <param name="Tukey" value="1"/> + <param name="Stdev" value="2"/> + </section> + <section name="Heavy"> + <param name="Tukey" value=""/> + <param name="Stdev" value="2"/> + </section> + <section name="Ratio"> + <param name="Tukey" value=""/> + <param name="Stdev" value=""/> + </section> + </section> + <section name="LabeledAggregation"> + <param name="labeledAggregationLight" value="Sum"/> + <param name="labeledAggregationHeavy" value="Median"/> + <param name="labeledAggregationRatio" value="Median"/> + </section> + </section> + <param name="outputParamfile" value="true"/> + <output name="out_paramfile" file="result_6.json"/> + </test> + </tests> + <help> + <![CDATA[ +What It Does +------------ +**Disclaimer** this tool needs a quantAndProt file, which combines the results from ProteinInference and PSMBasedQuantification. + +After quantification and protein inference are performed, it is known which peptide originated from which protein, as well as the intensity of each peptide. +The information available for each peptide now needs to be aggragated for their proteins. + +This tool performs the aggregation from the peptides to the protein in several steps. +The first step for the labeled protein quantification is the aggregation of the differently labeled peptides. Peptides with the same sequence, modifications and +charge are aggregated and the ratio between the intensity from the light and heavy version is calculated. +The next two aggregation steps are optional. One of them is the aggregation based on charge state. Similarily to the first step, peptides with the same sequence and +modifications, but different charge states are being aggregated. +The next optional step does the same for peptides with the same sequence, but different modifications. Those steps build upon each other. +The last step is the aggregation of all peptides of a protein. The result of each aggregation step is given as a tab separated file. +The aggregation is performed according to the given parameters for each step. If an optional aggregation is not performed, the next step takes the result from +the prior aggregation. For example, if aggregation by charge and modification are skipped, the protein aggregation gets a collection of peptides, where a peptidesequence can occur with different charge states and modifications. + +Further Reading +--------------- +Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html>`_. + ]]> + </help> +</tool> \ No newline at end of file