--- a/hardcoded_params.json	Fri Nov 06 20:19:49 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,236 +0,0 @@
-{
-	"#": "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}"
-	}],
-	"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",
-		"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",
-	"#": "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",
-		"tools": ["IDRipper"]
-	}],
-	"outputDirectory": [{
-		"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"]
-	
-	}]
-}