Mercurial > repos > galaxyp > openms_falsediscoveryrate
changeset 3:7e170e213707 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
| author | galaxyp |
|---|---|
| date | Wed, 09 Aug 2017 09:06:45 -0400 |
| parents | 518b1730cf2a |
| children | 3d0f0f347399 |
| files | FalseDiscoveryRate.xml datatypes_conf.xml filetypes.txt macros.xml readme.md tool.conf |
| diffstat | 6 files changed, 60 insertions(+), 65 deletions(-) [+] |
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--- a/FalseDiscoveryRate.xml Thu Apr 27 13:19:21 2017 -0400 +++ b/FalseDiscoveryRate.xml Wed Aug 09 09:06:45 2017 -0400 @@ -1,7 +1,7 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [ID Processing]--> -<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.1.0"> +<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.2.0"> <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description> <macros> <token name="@EXECUTABLE@">FalseDiscoveryRate</token> @@ -15,20 +15,30 @@ #if $param_in: -in $param_in #end if -#if $param_in_target: - -in_target $param_in_target -#end if -#if $param_in_decoy: - -in_decoy $param_in_decoy -#end if #if $param_out: -out $param_out #end if -#if $param_proteins_only: - -proteins_only +#if $param_PSM: + -PSM + #if " " in str($param_PSM): + "$param_PSM" + #else + $param_PSM + #end if #end if -#if $param_peptides_only: - -peptides_only +#if $param_protein: + -protein + #if " " in str($param_protein): + "$param_protein" + #else + $param_protein + #end if +#end if +#if $param_FDR_PSM: + -FDR:PSM $param_FDR_PSM +#end if +#if $param_FDR_protein: + -FDR:protein $param_FDR_protein #end if #if $param_algorithm_no_qvalues: -algorithm:no_qvalues @@ -52,11 +62,17 @@ #end if </command> <inputs> - <param name="param_in" type="data" format="idxml" optional="True" label="Identification input file containing a search against a concatenated sequence database" help="(-in) Either specify '-in' alone or 'in_target' together with 'in_decoy' as input"/> - <param name="param_in_target" type="data" format="idxml" optional="True" label="Identification input file containing a search against a target-only database" help="(-in_target) "/> - <param name="param_in_decoy" type="data" format="idxml" optional="True" label="Identification input file containing a search against a decoy-only database" help="(-in_decoy) "/> - <param name="param_proteins_only" display="radio" type="boolean" truevalue="-proteins_only" falsevalue="" checked="false" optional="True" label="If set only the FDR on protein level is calculated" help="(-proteins_only) "/> - <param name="param_peptides_only" display="radio" type="boolean" truevalue="-peptides_only" falsevalue="" checked="false" optional="True" label="If set only the FDR on peptide (PSM) level is calculated" help="(-peptides_only) "/> + <param name="param_in" type="data" format="idxml" optional="False" label="Identifications from searching a target-decoy database" help="(-in) "/> + <param name="param_PSM" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on PSM level" help="(-PSM) "> + <option value="true" selected="true">true</option> + <option value="false">false</option> + </param> + <param name="param_protein" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on protein level" help="(-protein) "> + <option value="true" selected="true">true</option> + <option value="false">false</option> + </param> + <param name="param_FDR_PSM" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter PSMs based on q-value (" help="(-PSM) e.g., 0.05 = 5% FDR, disabled for 1)"/> + <param name="param_FDR_protein" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter proteins based on q-value (" help="(-protein) e.g., 0.05 = 5% FDR, disabled for 1)"/> <param name="param_algorithm_no_qvalues" display="radio" type="boolean" truevalue="-algorithm:no_qvalues" falsevalue="" checked="false" optional="True" label="If 'true' strict FDRs will be calculated instead of q-values (the default)" help="(-no_qvalues) "/> <param name="param_algorithm_use_all_hits" display="radio" type="boolean" truevalue="-algorithm:use_all_hits" falsevalue="" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits) "/> <param name="param_algorithm_split_charge_variants" display="radio" type="boolean" truevalue="-algorithm:split_charge_variants" falsevalue="" checked="false" optional="True" label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" help="(-split_charge_variants) "/>
--- a/datatypes_conf.xml Thu Apr 27 13:19:21 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<datatypes> - <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> - <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml"/> - <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/> - <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXM" mimetype="application/xml"/> - <datatype extension="txt" type="galaxy.datatypes.data:Text"/> - <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> - <datatype extension="txt" type="galaxy.datatypes.data:Text"/> - <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/> - <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf"/> - <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml"/> - <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> - <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/> - <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp"/> - <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/> - <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> - <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/> - <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> - <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml"/> - <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> - <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml"/> - <datatype extension="grid" type="galaxy.datatypes.data:Grid"/> - <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml"/> - <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> - <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> - <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml"/> - <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/> - <datatype extension="txt" type="galaxy.datatypes.data:Text"/> - <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml"/> - <datatype extension="txt" type="galaxy.datatypes.data:Text"/> - </registration> -</datatypes>
--- a/filetypes.txt Thu Apr 27 13:19:21 2017 -0400 +++ b/filetypes.txt Wed Aug 09 09:06:45 2017 -0400 @@ -14,7 +14,7 @@ consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml edta tabular galaxy.datatypes.tabular:Tabular featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml -idXML idxml galaxy.datatypes.proteomics:IdXM application/xml +idXML idxml galaxy.datatypes.proteomics:IdXML application/xml mzML mzml galaxy.datatypes.proteomics:MzML application/xml mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml @@ -26,4 +26,4 @@ msp msp galaxy.datatypes.proteomics:Msp mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml png png galaxy.datatypes.images:Png image/png -mgf mgf galaxy.datatypes.proteomics:Mgf \ No newline at end of file +mgf mgf galaxy.datatypes.proteomics:Mgf
--- a/macros.xml Thu Apr 27 13:19:21 2017 -0400 +++ b/macros.xml Wed Aug 09 09:06:45 2017 -0400 @@ -2,7 +2,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.1">openms</requirement> + <requirement type="package" version="2.2">openms</requirement> <requirement type="package" version="15.12.15.2">xtandem</requirement> <requirement type="package" version="1.0">fido</requirement> <requirement type="package" version="2016.10.26">msgf_plus</requirement>
--- a/readme.md Thu Apr 27 13:19:21 2017 -0400 +++ b/readme.md Wed Aug 09 09:06:45 2017 -0400 @@ -14,15 +14,29 @@ Generating OpenMS wrappers ========================== - * install OpenMS (you can do this automatically through the Tool Shed) + * install OpenMS (you can do this automatically through Conda) * create a folder called CTD - * inside of your new installed openms/bin folder, execute the following command: + * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory: ```bash for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; ``` - * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). + * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow: + + ```bash + ls >> tools.txt + ``` + + * search for the `bin` folder of your conda environment containing OpenMS and do: + + ```bash + while read p; do + ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD; + done <tools.txt + ``` + + * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). * clone or install CTDopts @@ -42,7 +56,7 @@ git clone https://github.com/WorkflowConversion/CTD2Galaxy.git ``` - * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. + * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. ```bash python generator.py \
--- a/tool.conf Thu Apr 27 13:19:21 2017 -0400 +++ b/tool.conf Wed Aug 09 09:06:45 2017 -0400 @@ -6,13 +6,7 @@ <tool file="openms/RTModel.xml"/> <tool file="openms/RTPredict.xml"/> </section> - <section id="section-id-DEFAULT" name="DEFAULT"> - <tool file="openms/OpenSwathFileSplitter.xml"/> - <tool file="openms/OpenSwathMzMLFileCacher.xml"/> - </section> <section id="section-id-TargetedExperiments" name="Targeted Experiments"> - <tool file="openms/ConvertTraMLToTSV.xml"/> - <tool file="openms/ConvertTSVToTraML.xml"/> <tool file="openms/InclusionExclusionListCreator.xml"/> <tool file="openms/MRMMapper.xml"/> <tool file="openms/OpenSwathAnalyzer.xml"/> @@ -22,13 +16,17 @@ <tool file="openms/OpenSwathDecoyGenerator.xml"/> <tool file="openms/OpenSwathDIAPreScoring.xml"/> <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/> + <tool file="openms/OpenSwathFileSplitter.xml"/> + <tool file="openms/OpenSwathMzMLFileCacher.xml"/> <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/> <tool file="openms/OpenSwathRTNormalizer.xml"/> <tool file="openms/PrecursorIonSelector.xml"/> + <tool file="openms/TargetedFileConverter.xml"/> </section> <section id="section-id-Utilities" name="Utilities"> <tool file="openms/AccurateMassSearch.xml"/> <tool file="openms/CVInspector.xml"/> + <tool file="openms/DatabaseFilter.xml"/> <tool file="openms/DecoyDatabase.xml"/> <tool file="openms/DeMeanderize.xml"/> <tool file="openms/Digestor.xml"/> @@ -44,7 +42,6 @@ <tool file="openms/LabeledEval.xml"/> <tool file="openms/LowMemPeakPickerHiRes.xml"/> <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/> - <tool file="openms/MapAlignmentEvaluation.xml"/> <tool file="openms/MassCalculator.xml"/> <tool file="openms/MetaboliteSpectralMatcher.xml"/> <tool file="openms/MetaProSIP.xml"/> @@ -62,12 +59,14 @@ <tool file="openms/QCMerger.xml"/> <tool file="openms/QCShrinker.xml"/> <tool file="openms/RNPxl.xml"/> + <tool file="openms/RNPxlSearch.xml"/> <tool file="openms/RNPxlXICFilter.xml"/> <tool file="openms/RTEvaluation.xml"/> <tool file="openms/SemanticValidator.xml"/> <tool file="openms/SequenceCoverageCalculator.xml"/> <tool file="openms/SimpleSearchEngine.xml"/> <tool file="openms/SpecLibCreator.xml"/> + <tool file="openms/SpectraSTSearchAdapter.xml"/> <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/> <tool file="openms/TICCalculator.xml"/> <tool file="openms/TopPerc.xml"/> @@ -78,6 +77,7 @@ <tool file="openms/ConsensusMapNormalizer.xml"/> <tool file="openms/FeatureLinkerLabeled.xml"/> <tool file="openms/FeatureLinkerUnlabeled.xml"/> + <tool file="openms/FeatureLinkerUnlabeledKD.xml"/> <tool file="openms/FeatureLinkerUnlabeledQT.xml"/> <tool file="openms/MapRTTransformer.xml"/> </section> @@ -154,9 +154,7 @@ <tool file="openms/FeatureFinderMultiplex.xml"/> <tool file="openms/FeatureFinderSuperHirn.xml"/> <tool file="openms/IsobaricAnalyzer.xml"/> - <tool file="openms/ITRAQAnalyzer.xml"/> <tool file="openms/ProteinQuantifier.xml"/> <tool file="openms/ProteinResolver.xml"/> - <tool file="openms/TMTAnalyzer.xml"/> </section> </toolbox>