| Previous changeset 0:7c2b85eb3ccf (2017-03-01) Next changeset 2:7d0ac73772ea (2017-10-18) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 |
|
modified:
MSSimulator.xml filetypes.txt macros.xml readme.md tool.conf |
|
removed:
datatypes_conf.xml |
| b |
| diff -r 7c2b85eb3ccf -r a4c3db6825f4 MSSimulator.xml --- a/MSSimulator.xml Wed Mar 01 12:59:29 2017 -0500 +++ b/MSSimulator.xml Wed Aug 09 09:59:36 2017 -0400 |
| [ |
| 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: [Utilities]-->\n-<tool id="MSSimulator" name="MSSimulator" version="2.1.0">\n+<tool id="MSSimulator" name="MSSimulator" version="2.2.0">\n <description>A highly configurable simulator for mass spectrometry experiments.</description>\n <macros>\n <token name="@EXECUTABLE@">MSSimulator</token>\n@@ -38,10 +38,20 @@\n -out_id $param_out_id\n #end if\n #if $param_algorithm_MSSim_Digestion_enzyme:\n- -algorithm:MSSim:Digestion:enzyme $param_algorithm_MSSim_Digestion_enzyme\n+ -algorithm:MSSim:Digestion:enzyme\n+ #if " " in str($param_algorithm_MSSim_Digestion_enzyme):\n+ "$param_algorithm_MSSim_Digestion_enzyme"\n+ #else\n+ $param_algorithm_MSSim_Digestion_enzyme\n+ #end if\n #end if\n #if $param_algorithm_MSSim_Digestion_model:\n- -algorithm:MSSim:Digestion:model $param_algorithm_MSSim_Digestion_model\n+ -algorithm:MSSim:Digestion:model\n+ #if " " in str($param_algorithm_MSSim_Digestion_model):\n+ "$param_algorithm_MSSim_Digestion_model"\n+ #else\n+ $param_algorithm_MSSim_Digestion_model\n+ #end if\n #end if\n #if $param_algorithm_MSSim_Digestion_min_peptide_length:\n -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length\n@@ -53,10 +63,20 @@\n -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages\n #end if\n #if $param_algorithm_MSSim_RT_rt_column:\n- -algorithm:MSSim:RT:rt_column $param_algorithm_MSSim_RT_rt_column\n+ -algorithm:MSSim:RT:rt_column\n+ #if " " in str($param_algorithm_MSSim_RT_rt_column):\n+ "$param_algorithm_MSSim_RT_rt_column"\n+ #else\n+ $param_algorithm_MSSim_RT_rt_column\n+ #end if\n #end if\n #if $param_algorithm_MSSim_RT_auto_scale:\n- -algorithm:MSSim:RT:auto_scale $param_algorithm_MSSim_RT_auto_scale\n+ -algorithm:MSSim:RT:auto_scale\n+ #if " " in str($param_algorithm_MSSim_RT_auto_scale):\n+ "$param_algorithm_MSSim_RT_auto_scale"\n+ #else\n+ $param_algorithm_MSSim_RT_auto_scale\n+ #end if\n #end if\n #if $param_algorithm_MSSim_RT_total_gradient_time:\n -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time\n@@ -167,16 +187,31 @@\n -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit\n #end if\n #if $param_algorithm_MSSim_RawSignal_enabled:\n- -algorithm:MSSim:RawSignal:enabled $param_algorithm_MSSim_RawSignal_enabled\n+ -algorithm:MSSim:RawSignal:enabled\n+ #if " " in str($param_algorithm_MSSim_RawSignal_enabled):\n+ "$param_algorithm_MSSim_RawSignal_enabled"\n+ #else\n+ $param_algorithm_MSSim_RawSignal_enabled\n+ #end if\n #end if\n #if $param_algorithm_MSSim_RawSignal_peak_shape:\n- -algorithm:MSSim:RawSignal:peak_shape $param_algorithm_MSSim_RawSignal_peak_shape\n+ -algorithm:MSSim:RawSignal:peak_shape\n+ #if " " in str($param_algorithm_MSSim_RawSignal_peak_shape):\n+ "$param_algorithm_MSSim_RawSignal_peak_shape"\n+ #else\n+ $param_algorithm_MSSim_RawSignal_peak_shape\n+ #end if\n #end if\n #if $param_algorithm_MSSim_RawSignal_resolution_value:\n -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value\n #end if\n #if $param_algorithm_MSSim_RawSignal_resolution_type:\n- -algorithm:MSSim:RawSignal:resolution:type $param_algorithm_MSSim_RawSignal_resolution_type\n+ -algorithm:MSSim:RawSignal:resolution:type\n+ #if " " in str($param_algorithm_MSSim_RawSignal_resolution_type):\n+ "$param_algorithm_MSSim_RawSignal_resolution_type"\n+ #else\n+ $param_algorithm_MSSim_RawSignal_resolution_type\n+ #end if\n #end if\n #if $param_algorithm_MSSim_RawSignal_baseline_scaling:\n -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling\n@@ -221,7 +256,12 @@\n -algorithm:MSSim:RawSignal:nois'..b'</option>\n+ <option value="Arg-C">Arg-C</option>\n+ <option value="proline endopeptidase">proline endopeptidase</option>\n+ <option value="Trypsin" selected="true">Trypsin</option>\n+ <option value="2-iodobenzoate">2-iodobenzoate</option>\n <option value="no cleavage">no cleavage</option>\n <option value="unspecific cleavage">unspecific cleavage</option>\n- <option value="Trypsin" selected="true">Trypsin</option>\n- <option value="Trypsin/P">Trypsin/P</option>\n- <option value="CNBr">CNBr</option>\n- <option value="Formic_acid">Formic_acid</option>\n- <option value="Lys-C/P">Lys-C/P</option>\n- <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>\n- <option value="2-iodobenzoate">2-iodobenzoate</option>\n- <option value="proline endopeptidase">proline endopeptidase</option>\n- <option value="Chymotrypsin">Chymotrypsin</option>\n <option value="V8-E">V8-E</option>\n- <option value="V8-DE">V8-DE</option>\n- <option value="Asp-N_ambic">Asp-N_ambic</option>\n- <option value="TrypChymo">TrypChymo</option>\n- <option value="Arg-C">Arg-C</option>\n- <option value="Asp-N">Asp-N</option>\n- <option value="PepsinA">PepsinA</option>\n+ <option value="leukocyte elastase">leukocyte elastase</option>\n </param>\n <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)">\n <option value="trained">trained</option>\n@@ -747,6 +830,7 @@\n <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) "/>\n <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) "/>\n <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) "/>\n+ <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) "/>\n <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) "/>\n <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) "/>\n <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) ">\n' |
| b |
| diff -r 7c2b85eb3ccf -r a4c3db6825f4 datatypes_conf.xml --- a/datatypes_conf.xml Wed Mar 01 12:59:29 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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> |
| b |
| diff -r 7c2b85eb3ccf -r a4c3db6825f4 filetypes.txt --- a/filetypes.txt Wed Mar 01 12:59:29 2017 -0500 +++ b/filetypes.txt Wed Aug 09 09:59:36 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 7c2b85eb3ccf -r a4c3db6825f4 macros.xml --- a/macros.xml Wed Mar 01 12:59:29 2017 -0500 +++ b/macros.xml Wed Aug 09 09:59:36 2017 -0400 |
| b |
| @@ -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> |
| b |
| diff -r 7c2b85eb3ccf -r a4c3db6825f4 readme.md --- a/readme.md Wed Mar 01 12:59:29 2017 -0500 +++ b/readme.md Wed Aug 09 09:59:36 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 @@ -39,10 +53,10 @@ * clone or install CTD2Galaxy ```bash - git clone https://github.com/blankclemens/CTD2Galaxy.git + 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. + * 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 \ @@ -102,17 +116,32 @@ [...] ]]> ``` - * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line + + * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): - -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit - - and change it to + ``` + <command><![CDATA[ - -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" + ## check input file type + #set $in_type = $param_in.ext + + ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && + + IDFileConverter - * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: + #if $param_in: + -in 'param_in.${in_type}' + #end if + + [...] + ]]> + ``` + + * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: - <data name="param_out" metadata_source="param_in" auto_format="true"/> + - `<data name="param_out" auto_format="true"/>` + - `<data name="param_out" metadata_source="param_in" auto_format="true"/>` * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. |
| b |
| diff -r 7c2b85eb3ccf -r a4c3db6825f4 tool.conf --- a/tool.conf Wed Mar 01 12:59:29 2017 -0500 +++ b/tool.conf Wed Aug 09 09:59:36 2017 -0400 |
| b |
| @@ -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> |