| Previous changeset 0:566046627ebf (2017-03-01) Next changeset 2:797d5c59ef5b (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:
OpenSwathRTNormalizer.xml filetypes.txt macros.xml readme.md tool.conf |
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removed:
datatypes_conf.xml |
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| diff -r 566046627ebf -r 974dec16eb84 OpenSwathRTNormalizer.xml --- a/OpenSwathRTNormalizer.xml Wed Mar 01 12:16:05 2017 -0500 +++ b/OpenSwathRTNormalizer.xml Wed Aug 09 08:58:14 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: [Targeted Experiments]-->\n-<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.1.0">\n+<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.2.0">\n <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description>\n <macros>\n <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>\n@@ -65,7 +65,12 @@\n -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width\n #end if\n #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:\n- -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss\n+ -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss\n+ #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss):\n+ "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"\n+ #else\n+ $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss\n+ #end if\n #end if\n #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:\n -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width\n@@ -80,13 +85,23 @@\n -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count\n #end if\n #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:\n- -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages\n+ -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages\n+ #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages):\n+ "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages"\n+ #else\n+ $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages\n+ #end if\n #end if\n #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:\n -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks\n #end if\n #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:\n- -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method\n+ -algorithm:TransitionGroupPicker:PeakPickerMRM:method\n+ #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):\n+ "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"\n+ #else\n+ $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method\n+ #end if\n #end if\n #if $param_algorithm_DIAScoring_dia_extraction_window:\n -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window\n@@ -110,7 +125,12 @@\n -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff\n #end if\n #if $param_outlierDetection_outlierMethod:\n- -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod\n+ -outlierDetection:outlierMethod\n+ #if " " in str($param_outlierDetection_outlierMethod):\n+ "$param_outlierDetection_outlierMethod"\n+ #else\n+ $param_outlierDetection_outlierMethod\n+ #end if\n #end if\n #if $param_outlierDetection_useIterativeChauvenet:\n -outlierDetection:useIterativeChauvenet\n@@ -159,10 +179,18 @@\n -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width\n #end if\n #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:\n- -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_Trans'..b'easured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>\n <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>\n- <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad">\n- <sanitizer>\n- <valid initial="string.printable">\n- <remove value="\'"/>\n- <remove value="""/>\n- </valid>\n- </sanitizer>\n- </param>\n+ <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>\n <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/>\n <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/>\n <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>\n@@ -364,11 +432,12 @@\n <option value="true" selected="true">true</option>\n <option value="false">false</option>\n </param>\n- <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) ">\n+ <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) If turned off, will not use fragment ion spectra for scoring">\n <option value="true" selected="true">true</option>\n <option value="false">false</option>\n </param>\n <param name="param_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>\n+ <param name="param_algorithm_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/>\n <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/>\n <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>\n </expand>\n' |
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| diff -r 566046627ebf -r 974dec16eb84 datatypes_conf.xml --- a/datatypes_conf.xml Wed Mar 01 12:16:05 2017 -0500 +++ /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 566046627ebf -r 974dec16eb84 filetypes.txt --- a/filetypes.txt Wed Mar 01 12:16:05 2017 -0500 +++ b/filetypes.txt Wed Aug 09 08:58:14 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 566046627ebf -r 974dec16eb84 macros.xml --- a/macros.xml Wed Mar 01 12:16:05 2017 -0500 +++ b/macros.xml Wed Aug 09 08:58:14 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 566046627ebf -r 974dec16eb84 readme.md --- a/readme.md Wed Mar 01 12:16:05 2017 -0500 +++ b/readme.md Wed Aug 09 08:58:14 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 @@ -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. |
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| diff -r 566046627ebf -r 974dec16eb84 tool.conf --- a/tool.conf Wed Mar 01 12:16:05 2017 -0500 +++ b/tool.conf Wed Aug 09 08:58:14 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> |