Mercurial > repos > galaxyp > openms_idfileconverter
changeset 3:066cf4d993f5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
| author | galaxyp |
|---|---|
| date | Wed, 09 Aug 2017 09:10:41 -0400 |
| parents | 5588e443a7db |
| children | 4b4582790bbd |
| files | IDFileConverter.xml datatypes_conf.xml filetypes.txt macros.xml readme.md tool.conf |
| diffstat | 6 files changed, 83 insertions(+), 100 deletions(-) [+] |
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--- a/IDFileConverter.xml Thu Apr 27 13:23:15 2017 -0400 +++ b/IDFileConverter.xml Wed Aug 09 09:10:41 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: [ID Processing]--> -<tool id="IDFileConverter" name="IDFileConverter" version="2.1.0"> +<tool id="IDFileConverter" name="IDFileConverter" version="2.2.0"> <description>Converts identification engine file formats.</description> <macros> <token name="@EXECUTABLE@">IDFileConverter</token> @@ -11,68 +11,71 @@ <expand macro="stdio"/> <expand macro="requirements"/> <command><![CDATA[ - - ## check input file type - #set $in_type = $param_in.ext + +## 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.${in_type}' && - - IDFileConverter +## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files +ln -s '$param_in' 'param_in.${in_type}' && + +IDFileConverter - #if $param_in: - -in 'param_in.${in_type}' - #end if - #if $param_out: - -out $param_out - #end if - #if $param_out_type: - -out_type - #if " " in str($param_out_type): - "$param_out_type" - #else - $param_out_type - #end if - #end if - #if $param_mz_file: - -mz_file $param_mz_file +#if $param_in: + -in 'param_in.${in_type}' +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type #end if - #if $param_mz_name: - -mz_name "$param_mz_name" - #end if - #if $param_peptideprophet_analyzed: - -peptideprophet_analyzed +#end if +#if $param_mz_file: + -mz_file $param_mz_file +#end if +#if $param_mz_name: + -mz_name "$param_mz_name" +#end if +#if $param_peptideprophet_analyzed: + -peptideprophet_analyzed +#end if +#if $param_score_type: + -score_type + #if " " in str($param_score_type): + "$param_score_type" + #else + $param_score_type #end if - #if $param_score_type: - -score_type - #if " " in str($param_score_type): - "$param_score_type" - #else - $param_score_type - #end if - #end if - #if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_ignore_proteins_per_peptide: - -ignore_proteins_per_peptide - #end if - #if $adv_opts.param_scan_regex: - -scan_regex "$adv_opts.param_scan_regex" - #end if - #if $adv_opts.param_force: - -force - #end if - #end if - ]]> +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ignore_proteins_per_peptide: + -ignore_proteins_per_peptide +#end if + #if $adv_opts.param_scan_regex: + -scan_regex "$adv_opts.param_scan_regex" +#end if + #if $adv_opts.param_no_spectra_data_override: + -no_spectra_data_override +#end if + #if $adv_opts.param_force: + -force +#end if +#end if +]]> </command> <inputs> - <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), <br>- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), <br>- for Sequest results, a directory containing .out files. <br>"/> + <param name="param_in" type="data" format="pepxml,protXML,mascotXML,omssaXML,xml,psms,tabular,idxml,mzid" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), <br>- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), <br>- for Sequest results, a directory containing .out files. <br>"/> <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) "> <option value="idXML">idXML</option> <option value="mzid">mzid</option> <option value="pepXML">pepXML</option> <option value="FASTA">FASTA</option> </param> - <param name="param_mz_file" type="data" format="mzxml,mzml" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" help="(-mz_file) "/> + <param name="param_mz_file" type="data" format="mzml,mzxml,mzData" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file" help="(-mz_file) "/> <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'"> <sanitizer> <valid initial="string.printable"> @@ -97,6 +100,7 @@ </valid> </sanitizer> </param> + <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs>
--- a/datatypes_conf.xml Thu Apr 27 13:23:15 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>
--- a/filetypes.txt Thu Apr 27 13:23:15 2017 -0400 +++ b/filetypes.txt Wed Aug 09 09:10:41 2017 -0400 @@ -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
--- a/macros.xml Thu Apr 27 13:23:15 2017 -0400 +++ b/macros.xml Wed Aug 09 09:10:41 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 13:23:15 2017 -0400 +++ b/readme.md Wed Aug 09 09:10:41 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 13:23:15 2017 -0400 +++ b/tool.conf Wed Aug 09 09:10:41 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>