Mercurial > repos > galaxyp > proteomiqon_labelfreeproteinquantification
changeset 0:39fa1ddd587d 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 18:45:16 +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 18:45:16 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 18:45:16 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 18:45:16 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 18:45:16 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 18:45:16 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 18:45:16 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 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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 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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 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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 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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 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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 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