Mercurial > repos > galaxyp > openms_mssimulator
changeset 3:fcbdc271f48c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
author | galaxyp |
---|---|
date | Fri, 14 Jul 2017 18:56:04 -0400 |
parents | b8103b8deae2 |
children | f4a97c769c81 |
files | MSSimulator.xml macros.xml readme.md tool.conf |
diffstat | 4 files changed, 47 insertions(+), 31 deletions(-) [+] |
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--- a/MSSimulator.xml Thu Apr 27 12:58:04 2017 -0400 +++ b/MSSimulator.xml Fri Jul 14 18:56:04 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: [Utilities]--> -<tool id="MSSimulator" name="MSSimulator" version="2.1.0"> +<tool id="MSSimulator" name="MSSimulator" version="2.2.0"> <description>A highly configurable simulator for mass spectrometry experiments.</description> <macros> <token name="@EXECUTABLE@">MSSimulator</token> @@ -352,6 +352,9 @@ #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks: -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks #end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges +#end if #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions: -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions #end if @@ -623,26 +626,26 @@ </sanitizer> </param> <param name="param_algorithm_MSSim_Digestion_enzyme" type="select" optional="False" value="Trypsin" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="(-enzyme) "> - <option value="leukocyte elastase">leukocyte elastase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="Formic_acid">Formic_acid</option> + <option value="TrypChymo">TrypChymo</option> + <option value="V8-DE">V8-DE</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Asp-N">Asp-N</option> <option value="Lys-C">Lys-C</option> + <option value="PepsinA">PepsinA</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Arg-C">Arg-C</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="Trypsin" selected="true">Trypsin</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> <option value="no cleavage">no cleavage</option> <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Trypsin" selected="true">Trypsin</option> - <option value="Trypsin/P">Trypsin/P</option> - <option value="CNBr">CNBr</option> - <option value="Formic_acid">Formic_acid</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="Chymotrypsin">Chymotrypsin</option> <option value="V8-E">V8-E</option> - <option value="V8-DE">V8-DE</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="TrypChymo">TrypChymo</option> - <option value="Arg-C">Arg-C</option> - <option value="Asp-N">Asp-N</option> - <option value="PepsinA">PepsinA</option> + <option value="leukocyte elastase">leukocyte elastase</option> </param> <param name="param_algorithm_MSSim_Digestion_model" display="radio" type="select" optional="False" value="naive" label="The cleavage model to use for digestion" help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)"> <option value="trained">trained</option> @@ -827,6 +830,7 @@ <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/> <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses) "/> <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" falsevalue="" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks) "/> + <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" falsevalue="" checked="false" optional="True" label="Adds precursor peaks with all charges in the given range" help="(-add_all_precursor_charges) "/> <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" falsevalue="" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions) "/> <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/> <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions) ">
--- a/macros.xml Thu Apr 27 12:58:04 2017 -0400 +++ b/macros.xml Fri Jul 14 18:56:04 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 12:58:04 2017 -0400 +++ b/readme.md Fri Jul 14 18:56:04 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 12:58:04 2017 -0400 +++ b/tool.conf Fri Jul 14 18:56:04 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>