comparison hardcoded_params.json @ 13:31bc4129f589 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

12:f918cb7aefd5

		"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",

	    "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",

		"CTD:type": "output-prefix", 
		"CTD:advanced": false,
		"CTD:required": true,
		"CTD:restrictions": "mzml",
		"tools": ["OpenSwathFileSplitter"]
	}]
}

13:31bc4129f589

		"value":"${GALAXY_SLOTS:-1}"
	}],
	"threads": [{
		"value": "${GALAXY_SLOTS:-1}"
	}],
	"sirius:cores": [{
		"value": "${GALAXY_SLOTS:-1}"
	}],

	"#": "hardcode the outer loop threads for OpenSwathWorkflow",
	"outer_loop_threads": [{
			"value": "1", 
			"tools": ["OpenSwathWorkflow"]
	}],
	"separator": [{
		"value": ",",
		"tools": ["IDMassAccuracy"]
	}],

	"#": "don't alow to copy data internally to save computation time for reloading",
	"copy_data": [{
		"value": "false",
		"tools": ["MapAlignerTreeGuided"]
	}],

	"#": "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",

	    "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",
	"#": "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:type": "output-prefix", 
		"CTD:required": true,
		"CTD:restrictions": "mzml",
		"tools": ["MzMLSplitter"]
	}, {
		"value": "@", 
		"tools": ["IDRipper"]
	}],

	"#": "Try to remove xml data type whereever possible",
	"#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> 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",
	"#": "SeedListGenerator: remove consensusXML 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": "mzML,idXML,featureXML",
		"tools": ["SeedListGenerator"]
	}],

	"#": "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"]
	}],

	"#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527",
	"#": "output-prefix",
	"out_path": [{
		"CTD:type": "output-prefix", 
		"CTD:required": true,
		"CTD:restrictions": "idXML",

		"CTD:type": "output-prefix", 
		"CTD:advanced": false,
		"CTD:required": true,
		"CTD:restrictions": "mzml",
		"tools": ["OpenSwathFileSplitter"]
	}],

	"#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443",
        "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
	"output_files": [{
		"CTD:required": true,
		"tools": ["OpenSwathDIAPreScoring"]
	}, {
		"CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
		"tools": ["SpectraSTSearchAdapter"]
	
	}]
}