| Previous changeset 2:ca88bd28f116 (2017-04-27) Next changeset 4:e35b77c6d2e2 (2017-10-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 |
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modified:
FeatureFinderMultiplex.xml filetypes.txt macros.xml readme.md tool.conf |
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removed:
datatypes_conf.xml |
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| diff -r ca88bd28f116 -r 9ef0f56e82df FeatureFinderMultiplex.xml --- a/FeatureFinderMultiplex.xml Thu Apr 27 13:20:28 2017 -0400 +++ b/FeatureFinderMultiplex.xml Wed Aug 09 09:26:17 2017 -0400 |
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| @@ -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: [Quantitation]--> -<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.1.0"> +<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.2.0"> <description>Determination of peak ratios in LC-MS data</description> <macros> <token name="@EXECUTABLE@">FeatureFinderMultiplex</token> @@ -72,6 +72,14 @@ #if $adv_opts.param_algorithm_knock_out: -algorithm:knock_out #end if + #if $adv_opts.param_algorithm_spectrum_type: + -algorithm:spectrum_type + #if " " in str($adv_opts.param_algorithm_spectrum_type): + "$adv_opts.param_algorithm_spectrum_type" + #else + $adv_opts.param_algorithm_spectrum_type + #end if +#end if #if $adv_opts.param_algorithm_averagine_type: -algorithm:averagine_type #if " " in str($adv_opts.param_algorithm_averagine_type): @@ -165,6 +173,11 @@ </param> <param name="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="(-averagine_similarity_scaling) For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -> p' = p and x = 1 -> p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/> <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/> + <param name="param_algorithm_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Type of MS1 spectra in input mzML file" help="(-spectrum_type) 'automatic' determines the spectrum type directly from the input mzML file"> + <option value="profile">profile</option> + <option value="centroid">centroid</option> + <option value="automatic" selected="true">automatic</option> + </param> <param name="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) "> <option value="peptide" selected="true">peptide</option> <option value="RNA">RNA</option> |
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| diff -r ca88bd28f116 -r 9ef0f56e82df datatypes_conf.xml --- a/datatypes_conf.xml Thu Apr 27 13:20:28 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r ca88bd28f116 -r 9ef0f56e82df filetypes.txt --- a/filetypes.txt Thu Apr 27 13:20:28 2017 -0400 +++ b/filetypes.txt Wed Aug 09 09:26:17 2017 -0400 |
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| @@ -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 |
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| diff -r ca88bd28f116 -r 9ef0f56e82df macros.xml --- a/macros.xml Thu Apr 27 13:20:28 2017 -0400 +++ b/macros.xml Wed Aug 09 09:26:17 2017 -0400 |
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| @@ -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> |
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| diff -r ca88bd28f116 -r 9ef0f56e82df readme.md --- a/readme.md Thu Apr 27 13:20:28 2017 -0400 +++ b/readme.md Wed Aug 09 09:26:17 2017 -0400 |
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| @@ -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 \ |
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| diff -r ca88bd28f116 -r 9ef0f56e82df tool.conf --- a/tool.conf Thu Apr 27 13:20:28 2017 -0400 +++ b/tool.conf Wed Aug 09 09:26:17 2017 -0400 |
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| @@ -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> |