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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:
IDFilter.xml filetypes.txt macros.xml readme.md tool.conf |
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removed:
datatypes_conf.xml |
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| diff -r c427a8628cbe -r b6ec0f32ad4e IDFilter.xml --- a/IDFilter.xml Thu Apr 27 13:23:26 2017 -0400 +++ b/IDFilter.xml Wed Aug 09 09:17:44 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: [ID Processing]-->\n-<tool id="IDFilter" name="IDFilter" version="2.1.0">\n+<tool id="IDFilter" name="IDFilter" version="2.2.0">\n <description>Filters results from protein or peptide identification engines based on different criteria.</description>\n <macros>\n <token name="@EXECUTABLE@">IDFilter</token>\n@@ -54,12 +54,6 @@\n #if $param_score_prot:\n -score:prot $param_score_prot\n #end if\n-#if $param_thresh_pep:\n- -thresh:pep $param_thresh_pep\n-#end if\n-#if $param_thresh_prot:\n- -thresh:prot $param_thresh_prot\n-#end if\n #if $param_whitelist_proteins:\n -whitelist:proteins $param_whitelist_proteins\n #end if\n@@ -122,6 +116,31 @@\n #end if\n #end for\n #end if\n+#if $param_digest_fasta:\n+ -digest:fasta $param_digest_fasta\n+#end if\n+#if $param_digest_enzyme:\n+ -digest:enzyme\n+ #if " " in str($param_digest_enzyme):\n+ "$param_digest_enzyme"\n+ #else\n+ $param_digest_enzyme\n+ #end if\n+#end if\n+#if $param_digest_specificity:\n+ -digest:specificity\n+ #if " " in str($param_digest_specificity):\n+ "$param_digest_specificity"\n+ #else\n+ $param_digest_specificity\n+ #end if\n+#end if\n+#if $param_digest_missed_cleavages:\n+ -digest:missed_cleavages $param_digest_missed_cleavages\n+#end if\n+#if $param_digest_methionine_cleavage:\n+ -digest:methionine_cleavage\n+#end if\n #if $param_mz_error:\n -mz:error $param_mz_error\n #end if\n@@ -146,6 +165,12 @@\n #if $adv_opts.param_force:\n -force\n #end if\n+ #if $adv_opts.param_thresh_pep:\n+ -thresh:pep $adv_opts.param_thresh_pep\n+#end if\n+ #if $adv_opts.param_thresh_prot:\n+ -thresh:prot $adv_opts.param_thresh_prot\n+#end if\n #if $adv_opts.param_rt_p_value:\n -rt:p_value $adv_opts.param_rt_p_value\n #end if\n@@ -199,8 +224,6 @@\n </param>\n <param name="param_score_pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept" help="(-pep) "/>\n <param name="param_score_prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept" help="(-prot) Use in combination with \'delete_unreferenced_peptide_hits\' to remove affected peptides"/>\n- <param name="param_thresh_pep" type="float" value="0.0" label="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold" help="(-pep) "/>\n- <param name="param_thresh_prot" type="float" value="0.0" label="Keep a protein hit only if its score is above this fraction of the protein significance threshold" help="(-prot) Use in combination with \'delete_unreferenced_peptide_hits\' to remove affected peptides"/>\n <param name="param_whitelist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) <br>All peptides that are not referencing a protein in this file are removed. <br>All proteins whose accessions are not present in this file are removed"/>\n <repeat name="rep_param_whitelist_protein_accessions" min="0" max="1" title="param_whitelist_protein_accessions">\n <param name="param_whitelist_protein_accessions" type="text" size="30" label="All peptides that do not reference at least one of the provided protein accession are removed" help="(-protein_accessions) <br>Only proteins of the provided list are retained">\n@@ -216,6 +239,7 @@\n <param name="param_whitelist_ignore_modifications" display="radio" type="boolean" truevalue="-whitelist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare whitelisted peptides by sequence only" help="(-ignore_modifications) "/>\n <repeat name="rep_param_whitelist_modifications" min="0" max="1" title="param_whitelist_modifications">\n <param name="param_whitelist_modifications" type="select" op'..b'tional="False" value="Trypsin" label="Specify the digestion enzyme" help="(-enzyme) ">\n+ <option value="Formic_acid">Formic_acid</option>\n+ <option value="unspecific cleavage">unspecific cleavage</option>\n+ <option value="V8-DE">V8-DE</option>\n+ <option value="PepsinA">PepsinA</option>\n+ <option value="Asp-N">Asp-N</option>\n+ <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>\n+ <option value="Trypsin/P">Trypsin/P</option>\n+ <option value="2-iodobenzoate">2-iodobenzoate</option>\n+ <option value="TrypChymo">TrypChymo</option>\n+ <option value="Lys-C/P">Lys-C/P</option>\n+ <option value="Lys-C">Lys-C</option>\n+ <option value="CNBr">CNBr</option>\n+ <option value="V8-E">V8-E</option>\n+ <option value="proline endopeptidase">proline endopeptidase</option>\n+ <option value="Chymotrypsin">Chymotrypsin</option>\n+ <option value="leukocyte elastase">leukocyte elastase</option>\n+ <option value="Asp-N_ambic">Asp-N_ambic</option>\n+ <option value="no cleavage">no cleavage</option>\n+ <option value="Trypsin" selected="true">Trypsin</option>\n+ <option value="Arg-C">Arg-C</option>\n+ </param>\n+ <param name="param_digest_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the filte" help="(-specificity) ">\n+ <option value="full" selected="true">full</option>\n+ <option value="semi">semi</option>\n+ <option value="none">none</option>\n+ </param>\n+ <param name="param_digest_missed_cleavages" type="integer" min="-1" optional="True" value="-1" label="filter peptide evidences that have more than the specified missed_cleavages <br>By default missed cleavages are ignored" help="(-missed_cleavages) "/>\n+ <param name="param_digest_methionine_cleavage" display="radio" type="boolean" truevalue="-digest:methionine_cleavage" falsevalue="" checked="false" optional="True" label="Allow methionine cleavage at the protein start" help="(-methionine_cleavage) "/>\n <param name="param_mz_error" type="float" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)" help="(-error) "/>\n <param name="param_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Absolute or relative erro" help="(-unit) ">\n <option value="Da">Da</option>\n@@ -3437,6 +5356,8 @@\n <param name="param_best_strict" display="radio" type="boolean" truevalue="-best:strict" falsevalue="" checked="false" optional="True" label="Keep only the highest scoring peptide hit" help="(-strict) <br>Similar to n_peptide_hits=1, but if there are ties between two or more highest scoring hits, none are kept"/>\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+ <param name="param_thresh_pep" type="float" value="0.0" label="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold" help="(-pep) "/>\n+ <param name="param_thresh_prot" type="float" value="0.0" label="Keep a protein hit only if its score is above this fraction of the protein significance threshold" help="(-prot) Use in combination with \'delete_unreferenced_peptide_hits\' to remove affected peptides"/>\n <param name="param_rt_p_value" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict" help="(-p_value) "/>\n <param name="param_rt_p_value_1st_dim" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict for first dimension" help="(-p_value_1st_dim) "/>\n <param name="param_best_n_to_m_peptide_hits" type="text" size="30" value=":" label="Peptide hit rank range to extracts" help="(-n_to_m_peptide_hits) ">\n' |
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| diff -r c427a8628cbe -r b6ec0f32ad4e datatypes_conf.xml --- a/datatypes_conf.xml Thu Apr 27 13:23:26 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 c427a8628cbe -r b6ec0f32ad4e filetypes.txt --- a/filetypes.txt Thu Apr 27 13:23:26 2017 -0400 +++ b/filetypes.txt Wed Aug 09 09:17:44 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 c427a8628cbe -r b6ec0f32ad4e macros.xml --- a/macros.xml Thu Apr 27 13:23:26 2017 -0400 +++ b/macros.xml Wed Aug 09 09:17:44 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 c427a8628cbe -r b6ec0f32ad4e readme.md --- a/readme.md Thu Apr 27 13:23:26 2017 -0400 +++ b/readme.md Wed Aug 09 09:17:44 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 c427a8628cbe -r b6ec0f32ad4e tool.conf --- a/tool.conf Thu Apr 27 13:23:26 2017 -0400 +++ b/tool.conf Wed Aug 09 09:17:44 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> |