changeset 0:fd5af6775e87 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification commit 3d3272b1ebe527f4b1e80c08f915c6235625621c"
author galaxyp
date Wed, 13 Oct 2021 18:44:47 +0000
parents
children
files aggregationparams.xml labelfreeproteinquantification.xml test-data/result_1.json test-data/result_2.json test-data/result_3.json test-data/sample.quantAndProt
diffstat 6 files changed, 1269 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aggregationparams.xml	Wed Oct 13 18:44:47 2021 +0000
@@ -0,0 +1,51 @@
+<macros>
+    <xml name="AggregationParams">
+        <section name="Transform" title="Transforms">
+            <conditional name="TransformLightCond">
+                <param name="Type" type="select" label="Light">
+                    <option value="None">None</option>
+                    <option value="Log2">Log2</option>
+                    <option value="Substract">Substract</option>
+                    <option value="Add">Add</option>
+                    <option value="DivideBy">DivideBy</option>
+                    <option value="MultiplyBy">MultiplyBy</option>
+                </param>
+                <when value="None">
+                </when>
+                <when value="Log2">
+                </when>
+                <when value="Substract">
+                    <param name="Value" type="float" value="0.0" optional="true" label="Value" />
+                </when>
+                <when value="Add">
+                    <param name="Value" type="float" value="0.0" optional="true" label="Value" />
+                </when>
+                <when value="DivideBy">
+                    <param name="Value" type="float" value="0.0" optional="true" label="Value" />
+                </when>
+                <when value="MultiplyBy">
+                    <param name="Value" type="float" value="0.0" optional="true" label="Value" />
+                </when>
+            </conditional>
+        </section>
+        <section name="SingleFilters" title="Single filters">
+            <section name="Light" title="Light">
+                <param name="BiggerThan" type="float" value="" optional="true" label="Is bigger than" />
+                <param name="SmallerThan" type="float" value="" optional="true" label="Is smaller than" />
+            </section>
+        </section>
+        <section name="GroupFilters" title="Group Filters">
+            <section name="Light" title="Light">
+                <param name="Tukey" type="float" value="" optional="true" label="Tukey" />
+                <param name="Stdev" type="float" value="" optional="true" label="Stdev" />
+            </section>
+        </section>
+        <section name="Aggregation" title="Aggregation">
+            <param name="AggregationLight" type="select" label="Light">
+                <option value="Mean">Mean</option>
+                <option value="Median">Median</option>
+                <option value="Sum">Sum</option>
+            </param>
+        </section> 
+    </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/labelfreeproteinquantification.xml	Wed Oct 13 18:44:47 2021 +0000
@@ -0,0 +1,745 @@
+<tool id="proteomiqon_labelfreeproteinquantification" name="Proteomiqon LabelFreeProteinQuantification" 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-labelfreeproteinquantification</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_labelFreeQuant' 'LabelFreeQuant.txt' &&
+        proteomiqon-labelfreeproteinquantification -i './' -p '$paramfile' -o './'
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="paramfile">
+            <![CDATA[
+            {
+                "ModificationFilter": {
+                    "Case": "${ModificationFilterCond.ModificationFilter}",
+                    #if $ModificationFilterCond.ModificationFilter == "UseOnly"
+                    "Fields": [
+                        [
+                            #for $mod in $ModificationFilterCond.ModificationFilterSequence
+                            {
+                                "Case": "${mod}"
+                            },
+                            #end for
+                        ]
+                    ]
+                    #end if
+                },
+                #set $aggregationParams = $AggregatePeptideChargeStatesParams.AggregatePeptideChargeStatesParamsCond
+                #if $aggregationParams.AggregatePeptideChargeStatesParamsEnabled == "no"
+                "AggregatePeptideChargeStatesParams": null,
+                #else
+                "AggregatePeptideChargeStatesParams": {
+                    "Case": "Some",
+                    "Fields": [
+                        {
+                            #set $TransformSection = $aggregationParams.Transform
+                            #set $TransformLight = $TransformSection.TransformLightCond
+                            #if $TransformLight.Type == "None"
+                            "Transform": null,
+                            #else
+                            "Transform": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        #if $TransformLight.Type == "None"
+                                        "Light": null,
+                                        #else
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                {
+                                                    "Case": "${TransformLight.Type}",
+                                                    #if $TransformLight.Type != "Log2"
+                                                    "Fields": [
+                                                        $TransformLight.Value
+                                                    ]
+                                                    #end if
+                                                }
+                                            ]
+                                        },
+                                        #end if
+                                    }
+                                ]
+                            },
+                            #end if
+                            #set $SingleFiltersSection = $aggregationParams.SingleFilters
+                            #set $SingleFiltersLight = $SingleFiltersSection.Light
+                            #if not $SingleFiltersLight.BiggerThan and not $SingleFiltersLight.SmallerThan
+                            "SingleFilters": null,
+                            #else
+                            "SingleFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        #if not $SingleFiltersLight.BiggerThan and not $SingleFiltersLight.SmallerThan
+                                        "Light": null,
+                                        #else
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    #if $SingleFiltersLight.BiggerThan
+                                                    {
+                                                        "Case": "IsBiggerThan",
+                                                        "Fields": [
+                                                            $SingleFiltersLight.BiggerThan 
+                                                        ]
+                                                    },
+                                                    #end if
+                                                    #if $SingleFiltersLight.SmallerThan
+                                                    {
+                                                        "Case": "IsSmallerThan",
+                                                        "Fields": [
+                                                            $SingleFiltersLight.SmallerThan 
+                                                        ]
+                                                    }
+                                                    #end if
+                                                ]
+                                            ]
+                                        },
+                                        #end if
+                                    }
+                                ]
+                            },
+                            #end if
+                            #set $GroupFiltersSection = $aggregationParams.GroupFilters
+                            #set $GroupFiltersLight = $GroupFiltersSection.Light
+                            #if not $GroupFiltersLight.Tukey and not $GroupFiltersLight.Stdev
+                            "GroupFilters": null,
+                            #else
+                            "GroupFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        #if not $GroupFiltersLight.Tukey and not $GroupFiltersLight.Stdev
+                                        "Light": null,
+                                        #else
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    #if $GroupFiltersLight.Tukey
+                                                    {
+                                                        "Case": "Tukey",
+                                                        "Fields": [
+                                                        $GroupFiltersLight.Tukey
+                                                        ]
+                                                    },
+                                                    #end if
+                                                    #if $GroupFiltersLight.Stdev
+                                                    {
+                                                        "Case": "Stdev",
+                                                        "Fields": [
+                                                        $GroupFiltersLight.Stdev
+                                                        ]
+                                                    }
+                                                    #end if
+                                                ]
+                                            ]
+                                        },
+                                        #end if
+                                    }
+                                ]
+                            },
+                            #end if
+                            "Aggregation": {
+                                "Light": {
+                                    "Case": "${aggregationParams.Aggregation.AggregationLight}"
+                                }
+                            }
+                        }
+                    ]                    
+                },
+                #end if
+                #set $aggregationParams = $AggregateModifiedPeptidesParams.AggregateModifiedPeptidesParamsCond
+                #if $aggregationParams.AggregateModifiedPeptidesParamsEnabled == "no"
+                "AggregateModifiedPeptidesParams": null,
+                #else
+                "AggregateModifiedPeptidesParams": {
+                    "Case": "Some",
+                    "Fields": [
+                        {
+                            #set $TransformSection = $aggregationParams.Transform
+                            #set $TransformLight = $TransformSection.TransformLightCond
+                            #if $TransformLight.Type == "None"
+                            "Transform": null,
+                            #else
+                            "Transform": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        #if $TransformLight.Type == "None"
+                                        "Light": null,
+                                        #else
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                {
+                                                    "Case": "${TransformLight.Type}",
+                                                    #if $TransformLight.Type != "Log2"
+                                                    "Fields": [
+                                                        $TransformLight.Value
+                                                    ]
+                                                    #end if
+                                                }
+                                            ]
+                                        },
+                                        #end if
+                                    }
+                                ]
+                            },
+                            #end if
+                            #set $SingleFiltersSection = $aggregationParams.SingleFilters
+                            #set $SingleFiltersLight = $SingleFiltersSection.Light
+                            #if not $SingleFiltersLight.BiggerThan and not $SingleFiltersLight.SmallerThan
+                            "SingleFilters": null,
+                            #else
+                            "SingleFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        #if not $SingleFiltersLight.BiggerThan and not $SingleFiltersLight.SmallerThan
+                                        "Light": null,
+                                        #else
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    #if $SingleFiltersLight.BiggerThan
+                                                    {
+                                                        "Case": "IsBiggerThan",
+                                                        "Fields": [
+                                                            $SingleFiltersLight.BiggerThan 
+                                                        ]
+                                                    },
+                                                    #end if
+                                                    #if $SingleFiltersLight.SmallerThan
+                                                    {
+                                                        "Case": "IsSmallerThan",
+                                                        "Fields": [
+                                                            $SingleFiltersLight.SmallerThan 
+                                                        ]
+                                                    }
+                                                    #end if
+                                                ]
+                                            ]
+                                        },
+                                        #end if
+                                    }
+                                ]
+                            },
+                            #end if
+                            #set $GroupFiltersSection = $aggregationParams.GroupFilters
+                            #set $GroupFiltersLight = $GroupFiltersSection.Light
+                            #if not $GroupFiltersLight.Tukey and not $GroupFiltersLight.Stdev
+                            "GroupFilters": null,
+                            #else
+                            "GroupFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        #if not $GroupFiltersLight.Tukey and not $GroupFiltersLight.Stdev
+                                        "Light": null,
+                                        #else
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    #if $GroupFiltersLight.Tukey
+                                                    {
+                                                        "Case": "Tukey",
+                                                        "Fields": [
+                                                        $GroupFiltersLight.Tukey
+                                                        ]
+                                                    },
+                                                    #end if
+                                                    #if $GroupFiltersLight.Stdev
+                                                    {
+                                                        "Case": "Stdev",
+                                                        "Fields": [
+                                                        $GroupFiltersLight.Stdev
+                                                        ]
+                                                    }
+                                                    #end if
+                                                ]
+                                            ]
+                                        },
+                                        #end if
+                                    }
+                                ]
+                            },
+                            #end if
+                            "Aggregation": {
+                                "Light": {
+                                    "Case": "${aggregationParams.Aggregation.AggregationLight}"
+                                }
+                            }
+                        }
+                    ]                    
+                },
+                #end if
+                #set $aggregationParams = $AggregateToProteinGroupsParams
+                "AggregateToProteinGroupsParams": {
+                    #set $TransformSection = $aggregationParams.Transform
+                    #set $TransformLight = $TransformSection.TransformLightCond
+                    #if $TransformLight.Type == "None"
+                    "Transform": null,
+                    #else
+                    "Transform": {
+                        "Case": "Some",
+                        "Fields": [
+                            {
+                                #if $TransformLight.Type == "None"
+                                "Light": null,
+                                #else
+                                "Light": {
+                                    "Case": "Some",
+                                    "Fields": [
+                                        {
+                                            "Case": "${TransformLight.Type}",
+                                            #if $TransformLight.Type != "Log2"
+                                            "Fields": [
+                                                $TransformLight.Value
+                                            ]
+                                            #end if
+                                        }
+                                    ]
+                                },
+                                #end if
+                            }
+                        ]
+                    },
+                    #end if
+                    #set $SingleFiltersSection = $aggregationParams.SingleFilters
+                    #set $SingleFiltersLight = $SingleFiltersSection.Light
+                    #if not $SingleFiltersLight.BiggerThan and not $SingleFiltersLight.SmallerThan
+                    "SingleFilters": null,
+                    #else
+                    "SingleFilters": {
+                        "Case": "Some",
+                        "Fields": [
+                            {
+                                #if not $SingleFiltersLight.BiggerThan and not $SingleFiltersLight.SmallerThan
+                                "Light": null,
+                                #else
+                                "Light": {
+                                    "Case": "Some",
+                                    "Fields": [
+                                        [
+                                            #if $SingleFiltersLight.BiggerThan
+                                            {
+                                                "Case": "IsBiggerThan",
+                                                "Fields": [
+                                                    $SingleFiltersLight.BiggerThan 
+                                                ]
+                                            },
+                                            #end if
+                                            #if $SingleFiltersLight.SmallerThan
+                                            {
+                                                "Case": "IsSmallerThan",
+                                                "Fields": [
+                                                    $SingleFiltersLight.SmallerThan 
+                                                ]
+                                            }
+                                            #end if
+                                        ]
+                                    ]
+                                },
+                                #end if
+                            }
+                        ]
+                    },
+                    #end if
+                    #set $GroupFiltersSection = $aggregationParams.GroupFilters
+                    #set $GroupFiltersLight = $GroupFiltersSection.Light
+                    #if not $GroupFiltersLight.Tukey and not $GroupFiltersLight.Stdev
+                    "GroupFilters": null,
+                    #else
+                    "GroupFilters": {
+                        "Case": "Some",
+                        "Fields": [
+                            {
+                                #if not $GroupFiltersLight.Tukey and not $GroupFiltersLight.Stdev
+                                "Light": null,
+                                #else
+                                "Light": {
+                                    "Case": "Some",
+                                    "Fields": [
+                                        [
+                                            #if $GroupFiltersLight.Tukey
+                                            {
+                                                "Case": "Tukey",
+                                                "Fields": [
+                                                $GroupFiltersLight.Tukey
+                                                ]
+                                            },
+                                            #end if
+                                            #if $GroupFiltersLight.Stdev
+                                            {
+                                                "Case": "Stdev",
+                                                "Fields": [
+                                                $GroupFiltersLight.Stdev
+                                                ]
+                                            }
+                                            #end if
+                                        ]
+                                    ]
+                                },
+                                #end if
+                            }
+                        ]
+                    },
+                    #end if
+                    "Aggregation": {
+                        "Light": {
+                            "Case": "${aggregationParams.Aggregation.AggregationLight}"
+                        }
+                    }                   
+                },
+            }                
+            ]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="proteinassignedquantpepions" type="data" format="tabular" label="Protein assigned quant pep ions" help="Specify list of .quantAndProt files" multiple="true"/>
+        <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="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_labelFreeQuant" />
+        <data format="json" name="out_paramfile">
+            <filter>outputParamfile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="proteinassignedquantpepions" value="sample.quantAndProt"/>
+            <conditional name="ModificationFilterCond">
+                <param name="ModificationFilter" value="All"/>
+            </conditional>
+            <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="Transform">
+                    <conditional name="TransformLightCond">
+                        <param name="Type" value="None"/>
+                    </conditional>
+                </section>
+                <section name="SingleFilters">
+                    <section name="Light">
+                        <param name="BiggerThan" value=""/>
+                        <param name="SmallerThan" value=""/>
+                    </section>
+                </section>
+                <section name="GroupFilters">
+                    <section name="Light">
+                        <param name="Tukey" value=""/>
+                        <param name="Stdev" value=""/>
+                    </section>
+                </section>
+                <section name="Aggregation">
+                    <param name="AggregationLight" value="Mean"/>
+                </section>
+            </section>
+            <param name="outputParamfile" value="false"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="proteinassignedquantpepions" value="sample.quantAndProt"/>
+            <conditional name="ModificationFilterCond">
+                <param name="ModificationFilter" value="All"/>
+            </conditional>
+            <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="Transform">
+                    <conditional name="TransformLightCond">
+                        <param name="Type" value="None"/>
+                    </conditional>
+                </section>
+                <section name="SingleFilters">
+                    <section name="Light">
+                        <param name="BiggerThan" value=""/>
+                        <param name="SmallerThan" value=""/>
+                    </section>
+                </section>
+                <section name="GroupFilters">
+                    <section name="Light">
+                        <param name="Tukey" value=""/>
+                        <param name="Stdev" value=""/>
+                    </section>
+                </section>
+                <section name="Aggregation">
+                    <param name="AggregationLight" 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"/>
+            <conditional name="ModificationFilterCond">
+                <param name="ModificationFilter" value="No"/>
+            </conditional>
+            <section name="AggregatePeptideChargeStatesParams">
+                <conditional name="AggregatePeptideChargeStatesParamsCond">
+                    <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" />
+                    <section name="Transform">
+                        <conditional name="TransformLightCond">
+                            <param name="Type" value="Log2"/>
+                        </conditional>
+                    </section>
+                    <section name="SingleFilters">
+                        <section name="Light">
+                            <param name="BiggerThan" value="1"/>
+                            <param name="SmallerThan" value="2"/>
+                        </section>
+                    </section>
+                    <section name="GroupFilters">
+                        <section name="Light">
+                            <param name="Tukey" value="1"/>
+                            <param name="Stdev" value="2"/>
+                        </section>
+                    </section>
+                    <section name="Aggregation">
+                        <param name="AggregationLight" value="Median"/>
+                    </section>
+                </conditional>
+            </section>
+            <section name="AggregateModifiedPeptidesParams">
+                <conditional name="AggregateModifiedPeptidesParamsCond">
+                    <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/>
+                    <section name="Transform">
+                        <conditional name="TransformLightCond">
+                            <param name="Type" value="Log2"/>
+                        </conditional>
+                    </section>
+                    <section name="SingleFilters">
+                        <section name="Light">
+                            <param name="BiggerThan" value="1"/>
+                            <param name="SmallerThan" value="2"/>
+                        </section>
+                    </section>
+                    <section name="GroupFilters">
+                        <section name="Light">
+                            <param name="Tukey" value="1"/>
+                            <param name="Stdev" value="2"/>
+                        </section>
+                    </section>
+                    <section name="Aggregation">
+                        <param name="AggregationLight" value="Median"/>
+                    </section>
+                </conditional>
+            </section>
+            <section name="AggregateToProteinGroupsParams">
+                <section name="Transform">
+                    <conditional name="TransformLightCond">
+                        <param name="Type" value="Log2"/>
+                    </conditional>
+                </section>
+                <section name="SingleFilters">
+                    <section name="Light">
+                        <param name="BiggerThan" value="1"/>
+                        <param name="SmallerThan" value="2"/>
+                    </section>
+                </section>
+                <section name="GroupFilters">
+                    <section name="Light">
+                        <param name="Tukey" value="1"/>
+                        <param name="Stdev" value="2"/>
+                    </section>
+                </section>
+                <section name="Aggregation">
+                    <param name="AggregationLight" value="Median"/>
+                </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"/>
+            <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="AggregatePeptideChargeStatesParams">
+                <conditional name="AggregatePeptideChargeStatesParamsCond">
+                    <param name="AggregatePeptideChargeStatesParamsEnabled" value="yes" />
+                    <section name="Transform">
+                        <conditional name="TransformLightCond">
+                            <param name="Type" value="Substract"/>
+                            <param name="Value" value="2"/>
+                        </conditional>
+                    </section>
+                    <section name="SingleFilters">
+                        <section name="Light">
+                            <param name="BiggerThan" value="1"/>
+                            <param name="SmallerThan" value=""/>
+                        </section>
+                    </section>
+                    <section name="GroupFilters">
+                        <section name="Light">
+                            <param name="Tukey" value=""/>
+                            <param name="Stdev" value="2"/>
+                        </section>
+                    </section>
+                    <section name="Aggregation">
+                        <param name="AggregationLight" value="Median"/>
+                    </section>
+                </conditional>
+            </section>
+            <section name="AggregateModifiedPeptidesParams">
+                <conditional name="AggregateModifiedPeptidesParamsCond">
+                    <param name="AggregateModifiedPeptidesParamsEnabled" value="yes"/>
+                    <section name="Transform">
+                        <conditional name="TransformLightCond">
+                            <param name="Type" value="Add"/>
+                            <param name="Value" value="2"/>
+                        </conditional>
+                    </section>
+                    <section name="SingleFilters">
+                        <section name="Light">
+                            <param name="BiggerThan" value=""/>
+                            <param name="SmallerThan" value="2"/>
+                        </section>
+                    </section>
+                    <section name="GroupFilters">
+                        <section name="Light">
+                            <param name="Tukey" value="1"/>
+                            <param name="Stdev" value=""/>
+                        </section>
+                    </section>
+                    <section name="Aggregation">
+                        <param name="AggregationLight" value="Sum"/>
+                    </section>
+                </conditional>
+            </section>
+            <section name="AggregateToProteinGroupsParams">
+                <section name="Transform">
+                    <conditional name="TransformLightCond">
+                        <param name="Type" value="DivideBy"/>
+                        <param name="Value" value="2"/>
+                    </conditional>
+                </section>
+                <section name="SingleFilters">
+                    <section name="Light">
+                        <param name="BiggerThan" value=""/>
+                        <param name="SmallerThan" value=""/>
+                    </section>
+                </section>
+                <section name="GroupFilters">
+                    <section name="Light">
+                        <param name="Tukey" value=""/>
+                        <param name="Stdev" value=""/>
+                    </section>
+                </section>
+                <section name="Aggregation">
+                    <param name="AggregationLight" value="Mean"/>
+                </section>
+            </section>
+            <param name="outputParamfile" value="true"/>
+            <output name="out_paramfile" file="result_3.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 two aggregation steps are optional. One of them is the aggregation 
+based on charge state. 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 is performed on previously unaggregated 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/LabelFreeProteinQuantification.html>`_.  
+    ]]>
+    </help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result_1.json	Wed Oct 13 18:44:47 2021 +0000
@@ -0,0 +1,21 @@
+
+            
+            {
+                "ModificationFilter": {
+                    "Case": "All",
+                },
+                "AggregatePeptideChargeStatesParams": null,
+                "AggregateModifiedPeptidesParams": null,
+                "AggregateToProteinGroupsParams": {
+                    "Transform": null,
+                    "SingleFilters": null,
+                    "GroupFilters": null,
+                    "Aggregation": {
+                        "Light": {
+                            "Case": "Mean"
+                        }
+                    }                   
+                },
+            }                
+            
+        
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result_2.json	Wed Oct 13 18:44:47 2021 +0000
@@ -0,0 +1,241 @@
+
+            
+            {
+                "ModificationFilter": {
+                    "Case": "No",
+                },
+                "AggregatePeptideChargeStatesParams": {
+                    "Case": "Some",
+                    "Fields": [
+                        {
+                            "Transform": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                {
+                                                    "Case": "Log2",
+                                                }
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "SingleFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    {
+                                                        "Case": "IsBiggerThan",
+                                                        "Fields": [
+                                                            1.0 
+                                                        ]
+                                                    },
+                                                    {
+                                                        "Case": "IsSmallerThan",
+                                                        "Fields": [
+                                                            2.0 
+                                                        ]
+                                                    }
+                                                ]
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "GroupFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    {
+                                                        "Case": "Tukey",
+                                                        "Fields": [
+                                                        1.0
+                                                        ]
+                                                    },
+                                                    {
+                                                        "Case": "Stdev",
+                                                        "Fields": [
+                                                        2.0
+                                                        ]
+                                                    }
+                                                ]
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "Aggregation": {
+                                "Light": {
+                                    "Case": "Median"
+                                }
+                            }
+                        }
+                    ]                    
+                },
+                "AggregateModifiedPeptidesParams": {
+                    "Case": "Some",
+                    "Fields": [
+                        {
+                            "Transform": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                {
+                                                    "Case": "Log2",
+                                                }
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "SingleFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    {
+                                                        "Case": "IsBiggerThan",
+                                                        "Fields": [
+                                                            1.0 
+                                                        ]
+                                                    },
+                                                    {
+                                                        "Case": "IsSmallerThan",
+                                                        "Fields": [
+                                                            2.0 
+                                                        ]
+                                                    }
+                                                ]
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "GroupFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    {
+                                                        "Case": "Tukey",
+                                                        "Fields": [
+                                                        1.0
+                                                        ]
+                                                    },
+                                                    {
+                                                        "Case": "Stdev",
+                                                        "Fields": [
+                                                        2.0
+                                                        ]
+                                                    }
+                                                ]
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "Aggregation": {
+                                "Light": {
+                                    "Case": "Median"
+                                }
+                            }
+                        }
+                    ]                    
+                },
+                "AggregateToProteinGroupsParams": {
+                    "Transform": {
+                        "Case": "Some",
+                        "Fields": [
+                            {
+                                "Light": {
+                                    "Case": "Some",
+                                    "Fields": [
+                                        {
+                                            "Case": "Log2",
+                                        }
+                                    ]
+                                },
+                            }
+                        ]
+                    },
+                    "SingleFilters": {
+                        "Case": "Some",
+                        "Fields": [
+                            {
+                                "Light": {
+                                    "Case": "Some",
+                                    "Fields": [
+                                        [
+                                            {
+                                                "Case": "IsBiggerThan",
+                                                "Fields": [
+                                                    1.0 
+                                                ]
+                                            },
+                                            {
+                                                "Case": "IsSmallerThan",
+                                                "Fields": [
+                                                    2.0 
+                                                ]
+                                            }
+                                        ]
+                                    ]
+                                },
+                            }
+                        ]
+                    },
+                    "GroupFilters": {
+                        "Case": "Some",
+                        "Fields": [
+                            {
+                                "Light": {
+                                    "Case": "Some",
+                                    "Fields": [
+                                        [
+                                            {
+                                                "Case": "Tukey",
+                                                "Fields": [
+                                                1.0
+                                                ]
+                                            },
+                                            {
+                                                "Case": "Stdev",
+                                                "Fields": [
+                                                2.0
+                                                ]
+                                            }
+                                        ]
+                                    ]
+                                },
+                            }
+                        ]
+                    },
+                    "Aggregation": {
+                        "Light": {
+                            "Case": "Median"
+                        }
+                    }                   
+                },
+            }                
+            
+        
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result_3.json	Wed Oct 13 18:44:47 2021 +0000
@@ -0,0 +1,198 @@
+
+            
+            {
+                "ModificationFilter": {
+                    "Case": "UseOnly",
+                    "Fields": [
+                        [
+                            {
+                                "Case": "Acetylation'ProtNTerm'"
+                            },
+                            {
+                                "Case": "Carbamidomethyl'Cys'"
+                            },
+                            {
+                                "Case": "Oxidation'Met'"
+                            },
+                            {
+                                "Case": "Phosphorylation'Ser'Thr'Tyr'"
+                            },
+                            {
+                                "Case": "Pyro_Glu'GluNterm'"
+                            },
+                            {
+                                "Case": "Pyro_Glu'GlnNterm'"
+                            },
+                        ]
+                    ]
+                },
+                "AggregatePeptideChargeStatesParams": {
+                    "Case": "Some",
+                    "Fields": [
+                        {
+                            "Transform": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                {
+                                                    "Case": "Substract",
+                                                    "Fields": [
+                                                        2.0
+                                                    ]
+                                                }
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "SingleFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    {
+                                                        "Case": "IsBiggerThan",
+                                                        "Fields": [
+                                                            1.0 
+                                                        ]
+                                                    },
+                                                ]
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "GroupFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    {
+                                                        "Case": "Stdev",
+                                                        "Fields": [
+                                                        2.0
+                                                        ]
+                                                    }
+                                                ]
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "Aggregation": {
+                                "Light": {
+                                    "Case": "Median"
+                                }
+                            }
+                        }
+                    ]                    
+                },
+                "AggregateModifiedPeptidesParams": {
+                    "Case": "Some",
+                    "Fields": [
+                        {
+                            "Transform": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                {
+                                                    "Case": "Add",
+                                                    "Fields": [
+                                                        2.0
+                                                    ]
+                                                }
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "SingleFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    {
+                                                        "Case": "IsSmallerThan",
+                                                        "Fields": [
+                                                            2.0 
+                                                        ]
+                                                    }
+                                                ]
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "GroupFilters": {
+                                "Case": "Some",
+                                "Fields": [
+                                    {
+                                        "Light": {
+                                            "Case": "Some",
+                                            "Fields": [
+                                                [
+                                                    {
+                                                        "Case": "Tukey",
+                                                        "Fields": [
+                                                        1.0
+                                                        ]
+                                                    },
+                                                ]
+                                            ]
+                                        },
+                                    }
+                                ]
+                            },
+                            "Aggregation": {
+                                "Light": {
+                                    "Case": "Sum"
+                                }
+                            }
+                        }
+                    ]                    
+                },
+                "AggregateToProteinGroupsParams": {
+                    "Transform": {
+                        "Case": "Some",
+                        "Fields": [
+                            {
+                                "Light": {
+                                    "Case": "Some",
+                                    "Fields": [
+                                        {
+                                            "Case": "DivideBy",
+                                            "Fields": [
+                                                2.0
+                                            ]
+                                        }
+                                    ]
+                                },
+                            }
+                        ]
+                    },
+                    "SingleFilters": null,
+                    "GroupFilters": null,
+                    "Aggregation": {
+                        "Light": {
+                            "Case": "Mean"
+                        }
+                    }                   
+                },
+            }                
+            
+        
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.quantAndProt	Wed Oct 13 18:44:47 2021 +0000
@@ -0,0 +1,13 @@
+FileName	ProteinGroup	ProteinGroup_QValue	StringSequence	PepSequenceID	ModSequenceID	Charge	GlobalMod	PrecursorMZ	MeasuredMass	TheoMass	AbsDeltaMass	MeanPercolatorScore	QValue	PEPValue	ProteinNames	QuantMz_Light	Quant_Light	MeasuredApex_Light	Seo_Light	Params_Light	Difference_SearchRT_FittedRT_Light	KLDiv_Observed_Theoretical_Light	KLDiv_CorrectedObserved_Theoretical_Light	QuantMz_Heavy	Quant_Heavy	MeasuredApex_Heavy	Seo_Heavy	Params_Heavy	Difference_SearchRT_FittedRT_Heavy	KLDiv_Observed_Theoretical_Heavy	KLDiv_CorrectedObserved_Theoretical_Heavy	Correlation_Light_Heavy	QuantificationSource	IsotopicPatternMz_Light	IsotopicPatternIntensity_Observed_Light	IsotopicPatternIntensity_Corrected_Light	RtTrace_Light	IntensityTrace_Observed_Light	IntensityTrace_Corrected_Light	IsotopicPatternMz_Heavy	IsotopicPatternIntensity_Observed_Heavy	IsotopicPatternIntensity_Corrected_Heavy	RtTrace_Heavy	IntensityTrace_Observed_Heavy	IntensityTrace_Corrected_Heavy
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	ADGINPEELLGNSSAAAPR	201186	496415	3	0	627.9791917363045	1880.9157458084835	1880.92281879016	0.007072981676401469	27.123937606811523	0	0.002891455652662691	P0ACG1	627.9791917363045	2800.044190914148	7306.982208508748	597.1140223093846	8109.861419219218;82.06896519763045;0.13774045658792775	-0.07556519763045344	0.01596256310525423	0.023736834811431205	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	627.9808624404097;628.3155190116128;628.646802096179	0.3183042787047512;0.45858611394152016;0.22310960735372865	0.3143631148720035;0.4914319409801193;0.19420494414787726	80.000633333333;80.1283;80.1918;80.255633333333;80.319116666667;80.38295;80.446783333333;80.510283333333;80.573933333333;80.637266666667;80.700266666667;80.7626;80.825433333333;80.952416666667;81.015916666667;81.079416666667;81.14275;81.206233333333;81.269733333333;81.3334;81.3969;81.460233333333;81.523383333333;81.58655;81.649883333333;81.713033333333;81.77605;81.838866666667;81.902033333333;81.965366666667;82.0277;82.089683333333;82.151516666667;82.213516666667;82.275666666667;82.338;82.400833333333;82.464;82.527666666667;82.59115;82.654816666667;82.71865;82.78215;82.845633333333;82.909316666667;82.972633333333;83.099966666667;83.163466666667;83.22645;83.28945;83.352283333333;83.415266666667;83.478766666667;83.542266666667;83.6061;83.73325;83.79675;83.860083333333;83.923583333333;83.9869	2555.161376953125;0;3504.65771484375;9990.6650390625;21912.60546875;65444.88671875;90415.71875;83415.03125;42542.9140625;13058.21484375;3814.879638671875;3493.233154296875;2163.113037109375;1048.3873291015625;1421.603515625;2124.924560546875;2246.527099609375;1739.5709228515625;3076.027587890625;2232.805908203125;2186.531982421875;1436.9261474609375;1271.875732421875;1816.2874755859375;2279.58544921875;1857.84228515625;2863.480224609375;4091.864990234375;6306.556640625;8370.7958984375;10323.6552734375;9338.7685546875;8876.3408203125;6872.29541015625;3808.4013671875;4001.625244140625;1566.61962890625;2255.5078125;516.098876953125;1195.8431396484375;2531.072509765625;1661.6239013671875;4361.4404296875;15266.92578125;57596.9453125;115323.4609375;0;0;0;0;0;0;0;0;9858.28125;0;0;0;0;0	0;0;0;5978.274821592684;17971.087922668186;61574.260828865416;86616.0083860149;79686.26208779661;38885.10925334012;9471.391029961862;299.0450093947061;48.38697191134406;0;0;0;0;0;0;127.43367204615743;0;0;0;0;0;0;0;479.6755965407315;1778.501006819285;4063.6106690133224;6198.249556754909;8221.494227604948;7306.982208508748;6914.9219043994035;4981.239616579647;1987.7070037311212;2251.292985239107;0;645.910742509687;0;0;1132.6399127439745;333.6074378778094;3103.8597567966144;14079.80394410156;56480.30858912271;114277.3381348171;0;0;0;0;0;0;0;0;9447.523418148958;0;0;0;0;0						
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	EFSIDVLEEMLEK	201189	496420	2	0	791.3887547036785	1580.762956473737	1580.76437613404	0.0014196603030995902	25.120275497436523	0	0.0036220713345373524	P0ACG1	791.3887547036785	2576.418595239083	10210.23144281993	2665.3454235368536	11162.831789863221;122.37783934492137;0.0920772012874638	0.3311773550786228	0.004381567894722112	0.004512496536120306	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	791.389610918942;791.8996918771074	0.49546073268707164;0.5045392673129284	0.49476689619551073;0.5052331038044893	120.752766666667;120.816916666667;120.880916666667;120.94525;121.009583333333;121.07375;121.138066666667;121.202233333333;121.266233333333;121.330566666667;121.394716666667;121.458716666667;121.522716666667;121.58705;121.714033333333;121.7777;121.841366666667;121.905366666667;122.033516666667;122.161183333333;122.2255;122.289333333333;122.3535;122.4175;122.4815;122.545483333333;122.609983333333;122.674483333333;122.738316666667;122.802633333333;122.866466666667;122.930633333333;122.994966666667;123.059133333333;123.12345;123.188116666667;123.252283333333;123.316283333333;123.380433333333;123.444433333333;123.5086;123.572766666667;123.636933333333;123.700916666667;123.764916666667;123.82925;123.89375;123.9579;124.022066666667;124.0859;124.149566666667;124.213566666667;124.27805;124.406383333333;124.470216666667;124.5342;124.5987;124.662866666667	2246.7724609375;2988.921875;2871.395263671875;3777.080810546875;3560.402099609375;3447.984619140625;3363.421630859375;2338.849365234375;1882.1292724609375;2309.005615234375;1571.7860107421875;2336.082275390625;2943.489990234375;1155.0008544921875;2142.4560546875;1427.3931884765625;3002.325927734375;3720.367919921875;3013.584228515625;0;0;11441.7119140625;11787.3935546875;10519.5771484375;8650.2822265625;7671.6904296875;7386.8642578125;7230.01220703125;7108.93408203125;5519.73583984375;4334.13818359375;5730.88720703125;5460.69482421875;5164.19189453125;5078.83837890625;4040.382568359375;4640.9189453125;4356.2626953125;4316.93359375;5063.4375;4378.35498046875;3564.916748046875;3476.609619140625;3449.96826171875;3150.506591796875;3464.391357421875;2962.2646484375;2655.07958984375;1909.9754638671875;1527.7515869140625;1557.775146484375;1946.7105712890625;3661.521728515625;0;0;0;0;0	0;731.2903637181489;646.1686864176727;1584.2592129572927;1399.9854995491787;1319.972927489417;1267.8145815123194;275.64644910355173;0;310.60819899467674;0;402.4850853628336;1042.2908298824018;0;306.04955446670783;0;1230.7109712370195;1981.1506067095888;1306.7672492114507;0;0;9832.123087701699;10210.23144281993;8974.85641968299;7138.020600495527;6191.908228094368;5939.584047790311;5815.258491392493;5726.733002324598;4170.114885591131;3017.1259059537024;4446.513010293175;4208.988814946617;3945.1846592379457;3892.560773604135;2886.8655213010547;3520.1932623627836;3268.358915605125;3261.881813677969;4041.2672097976347;3389.0949011175994;2608.5946292123526;2553.2520697172627;2559.600619400467;2293.1527954143744;2640.073818962611;2171.004138388037;1896.8951051860736;1184.884119528497;835.7685209220156;898.9134607228812;1320.981289709857;3068.9337521925954;0;0;0;0;0						
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	ERREEEEQQQR	201221	496500	3	0	506.23813223670385	1515.6925673096814	1515.70259569619	0.010028386508565745	23.61475372314453	0	0.0044225330178454016	P0ACG1	506.23813223670385	2170.0302774331344	4334.595740530358	258.44682915984856	5496.891705223612;16.671903118418655;0.157492065306044;0.11816563179477606	0.08499902718718033	0.008664022458029025	0.01169940291231929	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	506.2365689830663;506.57156522231634;506.90817428913294	0.5518290515093405;0.31904157197508154;0.12912937651557796	0.5607567309710736;0.3184576142416523;0.12078565478727404	14.79445;14.856616666667;14.981266666667;15.043433333333;15.105766666667;15.1681;15.229766666667;15.29175;15.35375;15.415916666667;15.477916666667;15.539916666667;15.6019;15.6639;15.7259;15.7879;15.8499;15.973883333333;16.035216666667;16.097533333333;16.1592;16.220366666667;16.282533333333;16.3437;16.405016666667;16.466183333333;16.52735;16.588516666667;16.64985;16.711333333333;16.773166666667;16.835;16.896666666667;16.95865;17.020483333333;17.082316666667;17.14415;17.205983333333;17.2678;17.329633333333;17.391633333333;17.453633333333;17.515633333333;17.57745;17.639283333333;17.701116666667;17.824783333333;17.886766666667;17.9486;18.072266666667;18.134083333333;18.19575;18.31925;18.381066666667;18.442733333333;18.5044;18.566233333333;18.6279;18.68955;18.751383333333	432.7264709472656;517.094482421875;0;0;0;0;0;0;0;0;0;1081.1142578125;1082.0751953125;1465.668212890625;1098.1939697265625;999.1217041015625;1237.2269287109375;0;0;0;0;0;0;0;0;1549.5728759765625;1946.754150390625;2955.046142578125;3868.54296875;4624.689453125;4640.486328125;4197.3232421875;3792.86767578125;3050.314208984375;1962.7144775390625;1129.4605712890625;845.0803833007812;634.0119018554688;968.9420776367188;790.5789794921875;1056.9447021484375;1256.9581298828125;820.7520141601562;556.1218872070312;429.5687255859375;944.9432983398438;0;166.99365234375;173.62911987304688;0;0;101.58686065673828;0;0;0;0;0;0;0;0	346.3756821909526;430.5108118040217;0;0;0;0;0;0;0;0;0;992.2217259241747;992.9611360709954;1376.336620224137;1008.6494496844997;909.3694060377142;1147.2724948510017;0;0;0;0;0;0;0;0;1458.1380869883226;1855.205986875576;2863.3983087979964;3776.810083113305;4532.88690501712;4548.6300890676775;4105.429639194498;3700.9531639268434;2958.3951661318715;1870.807019293142;1037.5804030760207;753.2427068281773;542.2313632331062;877.2327297145093;698.9542547485835;965.4173688287948;1165.5402570516778;729.4549234303988;464.95609446283004;338.54390451003457;854.0682571657399;0;76.44102346458683;83.24735940879496;0;0;11.746318551724201;0;0;0;0;0;0;0;0						
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	ERREEEEQQQR	201221	496500	4	0	379.9295826079589	1515.6892245645954	1515.70259569619	0.013371131594567487	16.09270477294922	0.0002420867881135387	0.009964184814816432	P0ACG1	379.9295826079589	696.8486283034342	1687.324235610941	83.14198310933693	1748.6620190204349;16.768115341912257;0.15898005323276462	0.21308465808774457	0.008183354535709772	0.010997536254409017	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	379.92955619740115;380.43177671761606	0.8121866573732661;0.18781334262673388	0.8203604925882818;0.17963950741171822	14.981266666667;15.043433333333;15.105766666667;15.1681;15.229766666667;15.29175;15.35375;15.415916666667;15.477916666667;15.539916666667;15.6019;15.6639;15.7259;15.7879;15.8499;15.911883333333;15.973883333333;16.035216666667;16.097533333333;16.1592;16.220366666667;16.282533333333;16.3437;16.405016666667;16.466183333333;16.52735;16.588516666667;16.64985;16.711333333333;16.773166666667;16.835;16.896666666667;16.95865;17.020483333333;17.082316666667;17.14415;17.205983333333;17.2678;17.329633333333;17.391633333333;17.453633333333;17.515633333333;17.57745;17.639283333333;17.701116666667;17.76295;17.824783333333;17.886766666667;17.9486;18.010433333333;18.072266666667;18.134083333333;18.19575;18.257583333333;18.31925;18.381066666667;18.442733333333;18.5044;18.566233333333;18.6279;18.68955;18.751383333333;18.813216666667;18.87505;18.936883333333	56.5263557434082;44.071632385253906;26.278928756713867;31.890033721923828;16.150421142578125;0;3.558570146560669;0;0;0;0;22.583118438720703;14.644976615905762;31.342632293701172;6.0222392082214355;19.709247589111328;30.110837936401367;0;66.51819610595703;51.87349319458008;78.69992065429688;25.184049606323242;118.8019790649414;232.26515197753906;408.96661376953125;625.763916015625;889.096923828125;1262.205322265625;1693.6162109375;1891.11669921875;1514.5888671875;1347.19921875;906.8883666992188;548.706298828125;188.3299560546875;52.694271087646484;46.39823913574219;23.814809799194336;50.503997802734375;0;0;15.74006175994873;0;11.223278045654297;53.37881851196289;26.142114639282227;19.161731719970703;0;28.468555450439453;60.90681076049805;21.3515567779541;0;0;40.23966598510742;0;39.00776672363281;0;15.876830101013184;21.351545333862305;14.781644821166992;5.748498916625977;24.0886173248291;29.563867568969727;42.155208587646484;35.72260284423828	24.424578075203243;12.039015250539997;0;0;0;0;0;0;0;0;0;0;0;0.14840849196074402;0;0;0;0;35.70765579462111;21.14589047414462;48.05796284200473;0;88.34055519822772;201.89917973350606;378.6999236217832;595.6006077688078;859.0413476829298;1232.262049038758;1663.789989109615;1861.412393321346;1485.0113746134214;1317.7533766828178;877.578877862661;519.5376655984084;159.30643658157317;23.819853317557122;17.67663284643994;0;22.09802548584853;0;0;0;0;0;25.980748712660823;0;0;0;1.7762601145545425;34.39361950764281;0;0;0;14.44933413059195;0;13.581134365503718;0;0;0;0;0;0;5.413244088980832;18.1869181820147;11.936644916131364						
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	FTDVNGETK	201184	496412	2	0	505.73974689814446	1009.4649408626689	1009.4716397244902	0.006698861821291757	26.68318748474121	0	0.0030383985844686236	P0ACG1	505.73974689814446	5071.488135235683	58605.40802408641	2912.305730362216	67954.74602500195;28.907845897089388;0.029773211733516665	0.018154102910610703	0.0016175148327833323	0.0015358958145406075	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	505.7395696903701;506.2411373817241	0.6293800282374957;0.3706199717625043	0.6300782133496664;0.3699217866503336	26.972583333333;27.034733333333;27.158566666667;27.219883333333;27.34405;27.406216666667;27.467883333333;27.5297;27.591033333333;27.652366666667;27.714533333333;27.838516666667;27.900516666667;27.962683333333;28.025016666667;28.087333333333;28.1495;28.211833333333;28.274166666667;28.336;28.39815;28.45965;28.52165;28.644983333333;28.707133333333;28.830466666667;28.891633333333;28.952783333333;29.014783333333;29.077116666667;29.139616666667;29.201616666667;29.324933333333;29.3866;29.4486;29.510766666667;29.63525;29.696583333333;29.75825;29.8819;29.9434;30.0054;30.067233333333;30.129066666667;30.19105;30.253216666667;30.31555;30.3777;30.439366666667;30.501366666667;30.625533333333;30.68785;30.750183333333;30.81235;30.874016666667	2120.90625;896.776611328125;0;200.07504272460938;482.89422607421875;16.738616943359375;0;357.1993103027344;126.32930755615234;292.60931396484375;713.2907104492188;0;0;0;0;0;0;1269.61376953125;1445.518310546875;4797.5009765625;9951.9375;3582.742919921875;585.369873046875;0;263.08154296875;2454.423095703125;58856.375;21962.68359375;2906.029052734375;4584.64794921875;4664.84375;834.4066162109375;0;0;0;849.2581176757812;285.5043029785156;469.3174133300781;221.23513793945312;0;0;0;0;0;14.054034233093262;0;0;0;192.65365600585938;160.59841918945312;0;0;77.6917953491211;0;0	1766.12519556065;545.8994278930447;0;0;143.7279930341976;0;0;29.747677215633416;0;0;397.5749456497404;0;0;0;0;0;0;981.5512890515388;1161.4650639498261;4517.4795231689895;9675.973164774565;3310.8635675987343;317.6054243312736;0;3.6442094150780235;2199.201973235842;58605.408024086406;21716.010714699518;2663.6893054281354;4346.6783673090595;4431.279232725879;605.2797110642015;0;0;0;638.1564299550664;78.96617542563521;267.3616612403401;23.87856462158186;0;0;0;0;0;0;0;0;0;41.825533703771185;14.449197289259416;0;0;0;0;0						
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+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	REEEEQQQR	201202	496454	3	0	411.19023059713396	1230.5488623909719	1230.55889158686	0.01002919588813711	27.18474578857422	0	0.002914044337834602	P0ACG1	411.19023059713396	847.137383267882	4754.290603012805	206.13203921375188	5442.869175655345;11.970662191609843;0.06209205266329033	-0.014870751738317978	0.019652978036803687	0.020369253631384115	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	411.18899591944984;411.5251933384411;411.8589462924439	0.6277668221921373;0.23807002395545104;0.1341631538524117	0.6320995598546068;0.23666817619012784;0.13123226395526547	9.9634;10.0894;10.15255;10.214216666667;10.337216666667;10.4597;10.521366666667;10.583366666667;10.645533333333;10.708183333333;10.770183333333;10.83185;10.894683333333;10.9575;11.020183333333;11.082833333333;11.145833333333;11.207;11.26815;11.329483333333;11.390816666667;11.515316666667;11.5778;11.638966666667;11.763466666667;11.826283333333;11.887283333333;11.94845;12.011283333333;12.074116666667;12.136433333333;12.261266666667;12.386083333333;12.448583333333;12.510583333333;12.572916666667;12.697733333333;12.7604;12.822066666667;12.883066666667;13.004883333333;13.065883333333;13.12705;13.18905;13.2512;13.313383333333;13.3747;13.435866666667;13.497033333333;13.558016666667;13.619183333333;13.680516666667;13.74235;13.804666666667;13.927666666667	306.4140625;426.7331237792969;294.880859375;242.19692993164062;173.2835235595703;0;0;0;0;0;0;0;0;0;0;0;0;0;549.7486572265625;1013.790283203125;882.220703125;0;193.2176971435547;200.47964477539062;0;492.22833251953125;2097.505615234375;5297.67578125;4292.41943359375;1488.662109375;443.6770935058594;436.8423767089844;0;0;2189.37841796875;2330.072021484375;0;0;0;485.40142822265625;0;0;0;0;0;0;0;0;0;204.3234100341797;268.1127624511719;98.10391998291016;0;250.1753387451172;0	264.7187887850552;385.06276503300313;253.23540236141784;200.57632892575288;131.68768768551183;0;0;0;0;0;0;0;0;0;0;0;0;0;508.5099333069428;972.585586194083;841.0530321469907;0;152.13453665420667;159.44467526821558;0;451.30344204187355;2056.643366174807;5256.881747181544;4251.6994588440675;1448.0220461823062;403.12258943394835;396.3788022461275;0;0;2149.2168420195944;2290.019919168247;0;0;0;445.8216774183512;0;0;0;0;0;0;0;0;0;166.04346584873394;229.96588725520837;60.09029381087405;0;212.4285153477966;0						
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	SLDDFLI	201181	496410	2	0	411.7145234997518	821.4144940658836	821.41708497273	0.0025909068464216034	19.328554153442383	0.00018516232563881003	0.006938153112220831	P0ACG1	411.7145234997518	527.6675715399881	2180.728563623225	148.8644994669382	2834.946842300833;106.82634963233258;0.07425497407676283;0.0751670710003081	0.10841706766741765	0.003447772050624985	0.0038584108932188527	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	411.71162098377;412.2129123974631	0.7268887183604429;0.27311128163955706	0.7290573051629045;0.27094269483709554	104.940016666667;105.004016666667;105.068016666667;105.132183333333;105.196;105.260333333333;105.324166666667;105.38815;105.451983333333;105.51615;105.580316666667;105.644483333333;105.708466666667;105.7723;105.8363;105.900633333333;105.964633333333;106.02895;106.093116666667;106.157116666667;106.221283333333;106.2856;106.349766666667;106.4141;106.478433333333;106.542416666667;106.60675;106.67075;106.734916666667;106.799083333333;106.863233333333;106.9274;106.991566666667;107.056066666667;107.119883333333;107.184216666667;107.248216666667;107.312383333333;107.376716666667;107.441033333333;107.505033333333;107.569033333333;107.6332;107.697183333333;107.76135;107.825516666667;107.889516666667;107.953833333333;108.018;108.081833333333;108.146166666667;108.210166666667;108.27415;108.338316666667;108.402483333333;108.466483333333;108.5308;108.594966666667;108.658966666667;108.723133333333;108.787133333333;108.851283333333;108.915283333333	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;127.23267364501953;479.1552429199219;1500.292724609375;2363.71142578125;2017.3485107421875;1077.135009765625;741.4564819335938;196.4769744873047;73.51854705810547;64.11528015136719;52.574676513671875;6.269103527069092;49.58179473876953;0;0;6.554017543792725;0;0;0;0;0;0;0;0;0;0;0;0;8.121338844299316;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;117.51675798273273;469.41040745859056;1490.5223606392476;2353.919127303531;2007.5379999429194;1067.3100193197326;731.6206546279836;186.63380985536406;63.67136479866983;54.26721079702963;42.72865824721491;0;39.74791080730376;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0						
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	SVMLQSLNNIR	201190	496432	2	0	637.8448671762577	1273.6751814188954	1273.6812556512498	0.006074232354421838	26.68318748474121	0	0.0030383985844686236	P0ACG1	637.8448671762577	11908.525619507513	17418.977059949175	20120.85829685979	22644.670078167896;70.59096204027443;0.20979834771121486	0.15025462972556625	0.013325920016597645	0.012928011002134643	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	637.8419351839257;638.3406589638196	0.5198905347468559;0.4801094652531442	0.5211120247878958;0.4788879752121043	68.760633333333;68.823633333333;68.886616666667;68.949783333333;69.012616666667;69.074783333333;69.13695;69.2631;69.326433333333;69.3896;69.45275;69.515933333333;69.641583333333;69.704583333333;69.8309;69.893733333333;69.956566666667;70.082383333333;70.207216666667;70.269383333333;70.331866666667;70.394866666667;70.457866666667;70.521033333333;70.584016666667;70.64685;70.70985;70.773016666667;70.836016666667;70.897833333333;70.9595;71.021833333333;71.147816666667;71.27415;71.337483333333;71.400483333333;71.5268;71.590133333333;71.653633333333;71.71695;71.780116666667;71.842283333333;71.966283333333;72.090933333333;72.153933333333;72.2171;72.280433333333;72.343266666667;72.46775;72.530083333333;72.5929;72.7194	0;0;0;0;0;841.6626586914062;542.1353149414062;0;1736.1575927734375;870.7415771484375;1479.537353515625;1651.7691650390625;0;576.71435546875;0;0;715.9293212890625;926.0756225585938;0;0;20239.0078125;32259.154296875;39892.7734375;36142.22265625;18445.349609375;46663.359375;68032.1484375;14456.3154296875;2732.827880859375;1596.956787109375;4083.24267578125;6024.38720703125;3699.664306640625;1934.7686767578125;1526.5399169921875;572.4527587890625;832.6112060546875;660.4158935546875;3256.31005859375;7140.6044921875;2324.2421875;923.41796875;1116.1942138671875;2630.483154296875;2422.840087890625;2748.235107421875;1294.7796630859375;813.8204956054688;0;0;471.0208740234375;1391.060791015625	0;0;0;0;0;138.84499316025904;0;0;981.2974436076995;98.56769083860377;690.0730323044122;845.0416108053199;0;0;0;0;0;16.577138934371078;0;0;19278.895468804287;31282.33144059545;38899.33342087682;35132.26475055607;17418.977059949175;45620.677644633906;66973.26433548916;13381.334830797461;1641.8523766624833;490.08301691803786;2960.562244555317;4885.986660873863;2545.6249847701033;765.1664672083209;341.445129332486;0;0;0;2009.8382997656552;5878.91249611276;1047.3709410681004;0;0;1308.274966823112;1085.5722632899676;1395.9271449633543;0;0;0;0;0;0						
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	TPKPIAQALAEGK	201182	496411	3	0	441.9223309428637	1322.745163428161	1322.7558004899402	0.010637061779107171	26.880998611450195	0	0.002971550783745471	P0ACG1	441.9223309428637	9766.922981792948	43871.43754450883	906.0323896645378	47948.69974118925;49.0029417330888;0.08126265254101336	-0.12127506308879532	0.02746721555241951	0.026863734036194194	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	441.92231222153566;442.2594786645453;442.5969117923372	0.38394275211870754;0.419959003117068;0.19609824476422444	0.3846948892542357;0.42124639950884746;0.1940587112369169	46.9399;47.002066666667;47.0644;47.1264;47.188066666667;47.250716666667;47.31355;47.376383333333;47.438383333333;47.5002;47.562366666667;47.624033333333;47.6862;47.747866666667;47.810016666667;47.933683333333;47.996016666667;48.058666666667;48.121166666667;48.182833333333;48.244166666667;48.305666666667;48.366983333333;48.428983333333;48.49115;48.553316666667;48.615133333333;48.7393;48.801633333333;48.863966666667;48.92595;48.987783333333;49.04995;49.112783333333;49.175616666667;49.300766666667;49.362266666667;49.423766666667;49.48525;49.60875;49.671083333333;49.79625;49.858733333333;49.921566666667;49.9844;50.046716666667;50.108733333333;50.232383333333;50.35705;50.418866666667;50.4807;50.5427;50.605033333333;50.667683333333;50.730516666667;50.793516666667;50.856516666667	0;0;0;0;0;0;0;0;0;154.6994171142578;150.56463623046875;123.25760650634766;78.97238159179688;300.8324890136719;111.59588623046875;310.4272155761719;100.08187866210938;100.81901550292969;97.86841583251953;0;541.4420166015625;17.71348762512207;131.8187255859375;111.89118194580078;120.45211791992188;155.58535766601562;356.0449523925781;1781.6976318359375;3521.769287109375;11587.767578125;31280.2734375;47260.44921875;41716.41796875;19959.58203125;4697.6015625;0;0;0;154.99293518066406;0;185.69825744628906;0;0;5.314046382904053;0;0;330.0611267089844;146.28529357910156;0;602.551513671875;1186.0701904296875;5172.8125;14920.3056640625;39019.66015625;60144.99609375;6274.7431640625;1253.964599609375	400.37910139103116;368.09137910609223;335.8036368021983;303.51583605582596;271.2279216532704;238.93982320503522;206.65145676022775;174.36272642096407;142.07352595678785;264.4831575333643;228.05788398611992;168.45951919634297;91.88197013461492;281.44860922549435;59.91723423108202;226.4523137165365;0;0;0;0;295.95770162156725;0;0;0;0;0;0;1310.0368394050208;3017.8021660140466;11051.498821656187;30711.708856817524;46659.595190307635;41083.279898710025;19294.162022503453;3999.8963605026656;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;3921.7562678236054;13636.419879547793;37702.93693371837;58795.43246384266;4892.339188593676;0						
+Galaxy104-[HYE124_TTOF6600_DDA_1ug_Ecoli_lgillet_I150212_001.mzML]	P0ACG1	0	[ac]SVMLQSLNNIR	201190	496434	2	0	658.8514608677964	1315.6883688019727	1315.6918203343898	0.0034515324171024986	21.739656448364258	0.00012962602890660444	0.005294717979612006	P0ACG1	658.8514608677964	494.23213586744123	1228.9225061446894	619.0599016112824	1194.538394393447;95.19540846159765;0.16505965505675113	-0.2571084615976531	0.4212403632749776	0.42418291221924764	NaN	NaN	NaN	NaN		NaN	NaN	NaN	NaN	PSM	658.8449996528788;659.849553177578	0.32878938645897027;0.6712106135410297	0.32722814702678327;0.6727718529732167	92.949716666667;93.013716666667;93.077883333333;93.141866666667;93.205866666667;93.269533333333;93.333366666667;93.3972;93.52485;93.588683333333;93.7165;93.780166666667;93.843833333333;93.907666666667;93.97165;94.035333333333;94.09915;94.16315;94.227483333333;94.289633333333;94.351966666667;94.476966666667;94.5403;94.604116666667;94.668116666667;94.731783333333;94.795283333333;94.858933333333;94.9211;95.043933333333;95.167766666667;95.293583333333;95.35725;95.484066666667;95.547566666667;95.611233333333;95.674733333333;95.80205;95.865716666667;95.929383333333;95.993366666667;96.0572;96.1212;96.184866666667;96.248533333333;96.312183333333;96.376016666667;96.504183333333;96.568;96.631833333333;96.6955;96.823316666667;96.887316666667	0;0;0;0;0;0;0;695.8947143554688;0;1678.5333251953125;0;0;0;0;0;0;0;0;0;0;1011.1234130859375;0;0;0;0;0;0;0;222.95326232910156;910.5634155273438;1431.796142578125;0;1814.614990234375;0;0;0;244.9431915283203;0;0;0;0;0;0;0;0;0;469.1609802246094;0;0;0;2682.26171875;2206.258544921875;0	0;0;0;0;0;0;0;690.4669823786886;0;1671.873396248367;0;0;0;0;0;0;0;0;0;0;997.672701899161;0;0;0;0;0;0;0;204.52689540876924;891.5126004625985;1412.1204547607808;0;1793.6882288747624;0;0;0;221.50670056909257;0;0;0;0;0;0;0;0;0;439.3791483413522;0;0;0;2649.9175357712543;2173.2731766953893;0