| Previous changeset 2:d12500c4d67e (2017-04-27) Next changeset 4:6dc52aaeb90f (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:
FeatureFinderIdentification.xml filetypes.txt macros.xml readme.md tool.conf |
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removed:
datatypes_conf.xml |
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| diff -r d12500c4d67e -r c040ffc3ac9b FeatureFinderIdentification.xml --- a/FeatureFinderIdentification.xml Thu Apr 27 13:19:43 2017 -0400 +++ b/FeatureFinderIdentification.xml Wed Aug 09 09:54:55 2017 -0400 |
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| b'@@ -1,7 +1,7 @@\n <?xml version=\'1.0\' encoding=\'UTF-8\'?>\n <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->\n <!--Proposed Tool Section: [Quantitation]-->\n-<tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.1.0">\n+<tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.2.0">\n <description>Detects features in MS1 data based on peptide identifications.</description>\n <macros>\n <token name="@EXECUTABLE@">FeatureFinderIdentification</token>\n@@ -18,6 +18,9 @@\n #if $param_id:\n -id $param_id\n #end if\n+#if $param_id_ext:\n+ -id_ext $param_id_ext\n+#end if\n #if $param_out:\n -out $param_out\n #end if\n@@ -27,29 +30,63 @@\n #if $param_chrom_out:\n -chrom_out $param_chrom_out\n #end if\n-#if $param_trafo_out:\n- -trafo_out $param_trafo_out\n-#end if\n-#if $param_extract_reference_rt:\n- -extract:reference_rt\n- #if " " in str($param_extract_reference_rt):\n- "$param_extract_reference_rt"\n- #else\n- $param_extract_reference_rt\n- #end if\n-#end if\n-#if $param_extract_rt_window:\n- -extract:rt_window $param_extract_rt_window\n+#if $param_candidates_out:\n+ -candidates_out $param_candidates_out\n #end if\n #if $param_extract_mz_window:\n -extract:mz_window $param_extract_mz_window\n #end if\n-#if $param_extract_isotope_pmin:\n- -extract:isotope_pmin $param_extract_isotope_pmin\n+#if $param_extract_n_isotopes:\n+ -extract:n_isotopes $param_extract_n_isotopes\n #end if\n #if $param_detect_peak_width:\n -detect:peak_width $param_detect_peak_width\n #end if\n+#if $param_detect_mapping_tolerance:\n+ -detect:mapping_tolerance $param_detect_mapping_tolerance\n+#end if\n+#if $param_svm_samples:\n+ -svm:samples $param_svm_samples\n+#end if\n+#if $param_svm_no_selection:\n+ -svm:no_selection\n+#end if\n+#if $param_svm_xval_out:\n+ -svm:xval_out $param_svm_xval_out\n+#end if\n+#if $param_svm_kernel:\n+ -svm:kernel\n+ #if " " in str($param_svm_kernel):\n+ "$param_svm_kernel"\n+ #else\n+ $param_svm_kernel\n+ #end if\n+#end if\n+#if $param_svm_xval:\n+ -svm:xval $param_svm_xval\n+#end if\n+\n+#if $rep_param_svm_log2_C:\n+-svm:log2_C\n+ #for token in $rep_param_svm_log2_C:\n+ #if " " in str(token):\n+ "$token.param_svm_log2_C"\n+ #else\n+ $token.param_svm_log2_C\n+ #end if\n+ #end for\n+#end if\n+\n+#if $rep_param_svm_log2_gamma:\n+-svm:log2_gamma\n+ #for token in $rep_param_svm_log2_gamma:\n+ #if " " in str(token):\n+ "$token.param_svm_log2_gamma"\n+ #else\n+ $token.param_svm_log2_gamma\n+ #end if\n+ #end for\n+#end if\n #if $param_model_type:\n -model:type\n #if " " in str($param_model_type):\n@@ -59,11 +96,41 @@\n #end if\n #end if\n #if $adv_opts.adv_opts_selector==\'advanced\':\n+ #if $adv_opts.param_candidates_in:\n+ -candidates_in $adv_opts.param_candidates_in\n+#end if\n #if $adv_opts.param_force:\n -force\n #end if\n- #if $adv_opts.param_detect_all_features:\n- -detect:all_features\n+ #if $adv_opts.param_extract_isotope_pmin:\n+ -extract:isotope_pmin $adv_opts.param_extract_isotope_pmin\n+#end if\n+ #if $adv_opts.param_extract_rt_quantile:\n+ -extract:rt_quantile $adv_opts.param_extract_rt_quantile\n+#end if\n+ #if $adv_opts.param_extract_rt_window:\n+ -extract:rt_window $adv_opts.param_extract_rt_window\n+#end if\n+ #if $adv_opts.param_detect_min_peak_width:\n+ -detect:min_peak_width $adv_opts.param_detect_min_peak_width\n+#end if\n+ #if $adv_opts.param_detect_signal_to_noise:\n+ -detect:signal_to_noise $adv_opts.param_detect_signal_to_noise\n+#end if\n+ #if $adv_opts.param_svm_epsilon:\n+ -svm:epsilon $adv_opts.param_svm_epsilon\n+#end if\n+ #if $adv_opts.param_svm_cache_size:\n+ -svm:cache_size $adv_opts.param_svm_cache_size\n+#end if\n+ #if $adv_opts.param_svm_no_shrinking:\n+ -svm:no_shrinking\n+#end if\n+ #if $adv_opts.param_svm_predictors:\n+ -svm:predictors "$adv_opts.param_svm_predictors"\n+#end if\n+ #if $adv_opts.param_svm_min_prob'..b'nds if 1 or greater, else relative to \'peak_width\'"/>\n+ <param name="param_detect_signal_to_noise" type="float" min="0.1" optional="True" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help="(-signal_to_noise) "/>\n+ <param name="param_svm_epsilon" type="float" min="0.0" optional="True" value="0.001" label="Stopping criterion" help="(-epsilon) "/>\n+ <param name="param_svm_cache_size" type="float" min="1.0" optional="True" value="100.0" label="Size of the kernel cache (in MB)" help="(-cache_size) "/>\n+ <param name="param_svm_no_shrinking" display="radio" type="boolean" truevalue="-svm:no_shrinking" falsevalue="" checked="false" optional="True" label="Disable the shrinking heuristics" help="(-no_shrinking) "/>\n+ <param name="param_svm_predictors" type="text" size="30" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help="(-predictors) ">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="\'"/>\n+ <remove value="""/>\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="param_svm_min_prob" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help="(-min_prob) "/>\n <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; \'0\' to disable"/>\n <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/>\n <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help="(-no_imputation) "/>\n+ <param name="param_model_check_min_area" type="float" min="0.0" optional="True" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help="(-min_area) "/>\n <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries) "/>\n <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; \'0\' to disable" help="(-width) "/>\n <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; \'0\' to disable" help="(-asymmetry) "/>\n@@ -119,7 +228,8 @@\n <data name="param_out" format="featurexml"/>\n <data name="param_lib_out" format="traml"/>\n <data name="param_chrom_out" format="mzml"/>\n- <data name="param_trafo_out" format="trafoxml"/>\n+ <data name="param_candidates_out" format="featurexml"/>\n+ <data name="param_svm_xval_out" format="tabular"/>\n </outputs>\n <help>Detects features in MS1 data based on peptide identifications.\n \n' |
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| diff -r d12500c4d67e -r c040ffc3ac9b datatypes_conf.xml --- a/datatypes_conf.xml Thu Apr 27 13:19:43 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 d12500c4d67e -r c040ffc3ac9b filetypes.txt --- a/filetypes.txt Thu Apr 27 13:19:43 2017 -0400 +++ b/filetypes.txt Wed Aug 09 09:54:55 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 d12500c4d67e -r c040ffc3ac9b macros.xml --- a/macros.xml Thu Apr 27 13:19:43 2017 -0400 +++ b/macros.xml Wed Aug 09 09:54:55 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 d12500c4d67e -r c040ffc3ac9b readme.md --- a/readme.md Thu Apr 27 13:19:43 2017 -0400 +++ b/readme.md Wed Aug 09 09:54:55 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 d12500c4d67e -r c040ffc3ac9b tool.conf --- a/tool.conf Thu Apr 27 13:19:43 2017 -0400 +++ b/tool.conf Wed Aug 09 09:54:55 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> |