| Previous changeset 0:f9bc00c0ebed (2017-03-01) Next changeset 2:22e9bb7d151a (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:
XTandemAdapter.xml filetypes.txt macros.xml readme.md tool.conf |
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removed:
datatypes_conf.xml |
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| diff -r f9bc00c0ebed -r cd0746ee4796 XTandemAdapter.xml --- a/XTandemAdapter.xml Wed Mar 01 12:31:29 2017 -0500 +++ b/XTandemAdapter.xml Wed Aug 09 09:18:43 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: [Identification]-->\n-<tool id="XTandemAdapter" name="XTandemAdapter" version="2.1.0">\n+<tool id="XTandemAdapter" name="XTandemAdapter" version="2.2.0">\n <description>Annotates MS/MS spectra using X! Tandem.</description>\n <macros>\n <token name="@EXECUTABLE@">XTandemAdapter</token>\n@@ -19,6 +19,9 @@\n #if $param_out:\n -out $param_out\n #end if\n+#if $param_xml_out:\n+ -xml_out $param_xml_out\n+#end if\n #if $param_database:\n -database $param_database\n #end if\n@@ -35,19 +38,26 @@\n -fragment_mass_tolerance $param_fragment_mass_tolerance\n #end if\n #if $param_precursor_error_units:\n- -precursor_error_units $param_precursor_error_units\n+ -precursor_error_units\n+ #if " " in str($param_precursor_error_units):\n+ "$param_precursor_error_units"\n+ #else\n+ $param_precursor_error_units\n+ #end if\n #end if\n #if $param_fragment_error_units:\n- -fragment_error_units $param_fragment_error_units\n-#end if\n-#if $param_min_precursor_charge:\n- -min_precursor_charge $param_min_precursor_charge\n+ -fragment_error_units\n+ #if " " in str($param_fragment_error_units):\n+ "$param_fragment_error_units"\n+ #else\n+ $param_fragment_error_units\n+ #end if\n #end if\n #if $param_max_precursor_charge:\n -max_precursor_charge $param_max_precursor_charge\n #end if\n-#if $param_allow_isotope_error:\n- -allow_isotope_error $param_allow_isotope_error\n+#if $param_no_isotope_error:\n+ -no_isotope_error\n #end if\n \n #if $rep_param_fixed_modifications:\n@@ -71,30 +81,34 @@\n #end if\n #end for\n #end if\n-#if $param_missed_cleavages:\n- -missed_cleavages $param_missed_cleavages\n-#end if\n #if $param_minimum_fragment_mz:\n -minimum_fragment_mz $param_minimum_fragment_mz\n #end if\n-#if $param_cleavage_site:\n- -cleavage_site $param_cleavage_site\n+#if $param_enzyme:\n+ -enzyme\n+ #if " " in str($param_enzyme):\n+ "$param_enzyme"\n+ #else\n+ $param_enzyme\n+ #end if\n+#end if\n+#if $param_missed_cleavages:\n+ -missed_cleavages $param_missed_cleavages\n+#end if\n+#if $param_semi_cleavage:\n+ -semi_cleavage\n #end if\n #if $param_output_results:\n- -output_results $param_output_results\n+ -output_results\n+ #if " " in str($param_output_results):\n+ "$param_output_results"\n+ #else\n+ $param_output_results\n+ #end if\n #end if\n #if $param_max_valid_expect:\n -max_valid_expect $param_max_valid_expect\n #end if\n-#if $param_refinement:\n- -refinement\n-#end if\n-#if $param_use_noise_suppression:\n- -use_noise_suppression\n-#end if\n-#if $param_semi_cleavage:\n- -semi_cleavage\n-#end if\n #if $adv_opts.adv_opts_selector==\'advanced\':\n #if $adv_opts.param_force:\n -force\n@@ -102,10 +116,10 @@\n #end if\n </command>\n <inputs>\n- <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>\n+ <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing MS2 spectra" help="(-in) "/>\n <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file or pro file" help="(-database) Non-existing relative file-names are looked up via\'OpenMS.ini:id_db_dir\'"/>\n- <param name="param_default_config_file" type="data" format="" optional="True" value="CHEMISTRY/XTandem_default_input.xml" label="Default parameters input file, defaulting to the ones in the OpenMS/share folder.All parameters of this adapter take precedence over this file! Use it for parameters not available here!" help="(-default_config_file) "/>\n- <param name="param_ignore_adapter_param" display="radio" type="boolean" truevalue="-ignore_adapter_param" falsevalue="" checked="false" optional="True" label="The config given in \'default_config_file\' is used exclusively! No matter what other parameters (apart from -in,-out,-database,-xtandem_executable) are sayin'..b'benzoate</option>\n+ <option value="Asp-N">Asp-N</option>\n+ <option value="Arg-C">Arg-C</option>\n+ <option value="V8-E">V8-E</option>\n+ <option value="Lys-C">Lys-C</option>\n <option value="V8-DE">V8-DE</option>\n- <option value="Trypsin" selected="true">Trypsin</option>\n- <option value="Lys-C">Lys-C</option>\n- <option value="TrypChymo">TrypChymo</option>\n- <option value="Lys-C/P">Lys-C/P</option>\n+ <option value="leukocyte elastase">leukocyte elastase</option>\n <option value="Asp-N_ambic">Asp-N_ambic</option>\n+ <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>\n+ <option value="Chymotrypsin">Chymotrypsin</option>\n <option value="Trypsin/P">Trypsin/P</option>\n- <option value="Formic_acid">Formic_acid</option>\n- <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>\n- <option value="V8-E">V8-E</option>\n- <option value="leukocyte elastase">leukocyte elastase</option>\n- <option value="Arg-C">Arg-C</option>\n- <option value="Chymotrypsin">Chymotrypsin</option>\n- <option value="CNBr">CNBr</option>\n- <option value="Asp-N">Asp-N</option>\n- <option value="2-iodobenzoate">2-iodobenzoate</option>\n- <option value="PepsinA">PepsinA</option>\n+ <option value="Trypsin" selected="true">Trypsin</option>\n+ <option value="unspecific cleavage">unspecific cleavage</option>\n+ <option value="Lys-C/P">Lys-C/P</option>\n </param>\n+ <param name="param_missed_cleavages" type="integer" value="1" label="Number of possible cleavage sites missed by the enzyme" help="(-missed_cleavages) "/>\n+ <param name="param_semi_cleavage" display="radio" type="boolean" truevalue="-semi_cleavage" falsevalue="" checked="false" optional="True" label="Require only peptide end to have a valid cleavage site, not both" help="(-semi_cleavage) "/>\n <param name="param_output_results" display="radio" type="select" optional="False" value="all" label="Which hits should be reported" help="(-output_results) All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">\n <option value="all" selected="true">all</option>\n <option value="valid">valid</option>\n <option value="stochastic">stochastic</option>\n </param>\n- <param name="param_max_valid_expect" type="float" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if \'output_result\' is \'valid\' or \'stochastic\'" help="(-max_valid_expect) "/>\n- <param name="param_refinement" display="radio" type="boolean" truevalue="-refinement" falsevalue="" checked="false" optional="True" label="Enable the refinement" help="(-refinement) For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag"/>\n- <param name="param_use_noise_suppression" display="radio" type="boolean" truevalue="-use_noise_suppression" falsevalue="" checked="false" optional="True" label="Enable the use of the noise suppression routines" help="(-use_noise_suppression) "/>\n- <param name="param_semi_cleavage" display="radio" type="boolean" truevalue="-semi_cleavage" falsevalue="" checked="false" optional="True" label="If set, both termini must NOT follow the cutting rule" help="(-semi_cleavage) For most applications it is NOT recommended to set this flag"/>\n+ <param name="param_max_valid_expect" type="float" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if \'output_result\' is \'valid\' or \'stochastic\')" help="(-max_valid_expect) "/>\n <expand macro="advanced_options">\n <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>\n </expand>\n </inputs>\n <outputs>\n <data name="param_out" format="idxml"/>\n+ <data name="param_xml_out" format="xml"/>\n </outputs>\n <help>Annotates MS/MS spectra using X! Tandem.\n \n' |
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| diff -r f9bc00c0ebed -r cd0746ee4796 datatypes_conf.xml --- a/datatypes_conf.xml Wed Mar 01 12:31:29 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 f9bc00c0ebed -r cd0746ee4796 filetypes.txt --- a/filetypes.txt Wed Mar 01 12:31:29 2017 -0500 +++ b/filetypes.txt Wed Aug 09 09:18:43 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 f9bc00c0ebed -r cd0746ee4796 macros.xml --- a/macros.xml Wed Mar 01 12:31:29 2017 -0500 +++ b/macros.xml Wed Aug 09 09:18:43 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 f9bc00c0ebed -r cd0746ee4796 readme.md --- a/readme.md Wed Mar 01 12:31:29 2017 -0500 +++ b/readme.md Wed Aug 09 09:18:43 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 f9bc00c0ebed -r cd0746ee4796 tool.conf --- a/tool.conf Wed Mar 01 12:31:29 2017 -0500 +++ b/tool.conf Wed Aug 09 09:18:43 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> |