changeset 1:764e011f1b0e draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification commit 8061c6f26807bad85ed483dbe1a28054cbd631a2"
author galaxyp
date Fri, 17 Sep 2021 16:30:39 +0000
parents cbdfdca98db3
children
files labeledproteinquantification.xml proteomiqon_labeledproteinquantification.xml
diffstat 2 files changed, 2527 insertions(+), 2527 deletions(-) [+]
line wrap: on
line diff
--- a/labeledproteinquantification.xml	Thu Sep 16 21:11:34 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2527 +0,0 @@
-<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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteomiqon_labeledproteinquantification.xml	Fri Sep 17 16:30:39 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>
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