Mercurial > repos > galaxyp > openms_assaygeneratormetabo
view hardcoded_params.json @ 1:2c3d2c216ff9 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author | galaxyp |
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date | Thu, 24 Sep 2020 12:25:57 +0000 |
parents | cb9d2162b340 |
children | d30e724536fc |
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{ "#": "blacklist parameters", "version": [{"value": "@"}], "debug": [{"value": "@"}], "algorithm:debug": [{"value": "@"}], "java_memory": [{"value": "@"}], "java_permgen": [{"value": "@"}], "#": "type of input is always determined from the file extension ", "in_type": [{"value": "@"}], "#": "tool specific blacklist parameters", "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], "NET_executable": [{ "value": "@", "tools": ["FileConverter"] }], "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], "#": "TODO would need treatment as prefix-output", "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], "#": "hardcode parameter values", "comet_version": [{ "value":"2016.01 rev. 3" }], "comet_executable": [{ "value":"comet" }], "crux_executable": [{ "value": "crux" }], "fido_executable": [{ "value":"Fido" }], "fidocp_executable": [{ "value":"FidoChooseParameters" }], "maracluster_executable": [{ "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" }], "mascot_directory": [{ "value":"TODO" }], "myrimatch_executable": [{ "value":"myrimatch" }], "omssa_executable": [{ "value":"$(dirname $(realpath $(which omssacl)))/omssacl" }], "ThermoRaw_executable": [{ "value": "ThermoRawFileParser.exe", "tools": ["FileConverter"] }], "pepnovo_executable": [{ "value":"pepnovo" }], "percolator_executable": [{ "value":"percolator" }], "xtandem_executable": [{ "value":"xtandem" }], "executable": [ { "value":"$(dirname $(realpath $(which luciphor2)))/luciphor2.jar", "tools": ["LuciphorAdapter"] }, { "value":"/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", "tools": ["MSFraggerAdapter"] }, { "value":"$(msgf_plus -get_jar_path)", "tools": ["MSGFPlusAdapter"] }, { "value": "/home/berntm/Downloads/novor/lib/novor.jar", "tools": ["NovorAdapter"] }, { "value":"$(which sirius)", "tools": ["SiriusAdapter", "AssayGeneratorMetabo"] }, { "value":"spectrast", "tools": ["SpectraSTSearchAdapter"] } ], "r_executable": [{ "value":"R" }], "rscript_executable": [{ "value":"Rscript" }], "java_executable": [{ "value":"java" }], "log": [{ "value":"log.txt" }], "tempDirectory": [{ "value":"$TMP_DIR" }], "temp_data_directory": [{ "value":"$TMP_DIR" }], "algorithm:Preprocessing:tmp_dir": [{ "value":"$TMP_DIR" }], "no_progress": [{ "value": true }], "#": "only used in LuciphorAdapter at the moment, inconsistency will be fixed", "num_threads": [{ "value":"${GALAXY_SLOTS:-1}" }], "threads": [{ "value": "${GALAXY_SLOTS:-1}" }], "#": "hardcode the outer loop threads for OpenSwathWorkflow", "outer_loop_threads": [{ "value": "1", "tools": ["OpenSwathWorkflow"] }], "separator": [{ "value": ",", "tools": ["IDMassAccuracy"] }], "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)", "#": "test is not a hardcoded value since we need to set it in the tool tests", "test": [{ "CTD:type": "text", "XML:type": "hidden" }], "#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)", "#": "for some tools the user needs to select the desired output type since detection by extension makes no sense for galaxy tools", "out_type": [{ "CTD:required": true, "CTD:advanced": false }], "#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter", "#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here", "#": "MascotAdapter: https://github.com/OpenMS/OpenMS/pull/4553", "#": "Phosphoscoring: https://github.com/OpenMS/OpenMS/pull/4569", "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404", "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)", "out": [{ "CTD:is_list": false, "tools": ["SeedListGenerator"] }, { "CTD:required": true, "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"] }, { "CTD:restrictions": "idXML", "tools": ["MascotAdapter"] }, { "CTD:restrictions": "idXML", "tools": ["PhosphoScoring"] }, { "CTD:type": "output-prefix", "CTD:required": true, "CTD:restrictions": "mzml", "tools": ["MzMLSplitter"] }, { "value": "@", "tools": ["IDRipper"] }], "#": "https://github.com/OpenMS/OpenMS/pull/4552 .. if this is removed the test will need out_cm_FLAG", "out_cm": [{ "CTD:required": true, "tools": ["MetaboliteAdductDecharger"] }], "#": "https://github.com/OpenMS/OpenMS/pull/4451", "out_xquestxml": [{ "CTD:restrictions": "xquest.xml", "tools": ["OpenPepXL", "OpenPepXLLF"] }], "out_xquest_specxml": [{ "CTD:restrictions": "spec.xml", "tools": ["OpenPepXL", "OpenPepXLLF"] }], "#": "Try to remove xml data type whereever possible", "#": "XTandem Adapter output is called .xml in OMS -> use Galaxy's bioml", "xml_out": [{ "CTD:restrictions": "bioml", "tools": ["XTandemAdapter"] }], "#": "IDFileConverter remove xml", "#": "OpenSwathWorkflow make in single file input and all outputs non-optional", "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release", "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release", "#": "SeedListGenerator https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter", "in": [{ "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml", "tools": ["IDFileConverter"] }, { "CTD:is_list": false, "tools": ["OpenSwathWorkflow"] }, { "CTD:restrictions": "idXML,mzid,xquest.xml", "tools": ["XFDR"] }, { "CTD:restrictions": "txt,tsv,pep.xml,pepXML,html", "tools": ["SpectraSTSearchAdapter"] }, { "CTD:restrictions": "mzML,idXML,featureXML", "tools": ["SeedListGenerator"] }], "#": "parameter is a flag but restrictions in wrong order: TODO https://github.com/OpenMS/OpenMS/pull/4455", "# masstrace_snr_filtering": [{ "CTD:restrictions": "true,false", "tools": ["MassTraceExtractor"] }], "#": "IDMapper has in and spectra:in params, in is used in out as format_source", "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", "spectra:in": [{ "CTD:name": "_in", "tools": ["IDMapper"] }], "#": "output-prefix", "out_path": [{ "CTD:type": "output-prefix", "CTD:required": true, "CTD:restrictions": "idXML", "tools": ["IDRipper"] }], "outputDirectory": [{ "CTD:type": "output-prefix", "CTD:advanced": false, "CTD:required": true, "CTD:restrictions": "mzml", "tools": ["OpenSwathFileSplitter"] }] }