diff hardcoded_params.json @ 11:2c6f5858e89a draft

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

--- a/hardcoded_params.json	Wed Sep 23 15:06:30 2020 +0000
+++ b/hardcoded_params.json	Tue Oct 13 19:55:08 2020 +0000
@@ -119,6 +119,10 @@
 	"threads": [{
 		"value": "${GALAXY_SLOTS:-1}"
 	}],
+	"sirius:cores": [{
+		"value": "${GALAXY_SLOTS:-1}"
+	}],
+
 	"#": "hardcode the outer loop threads for OpenSwathWorkflow",
 	"outer_loop_threads": [{
 			"value": "1", 
@@ -128,6 +132,13 @@
 		"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", 
@@ -146,8 +157,6 @@
 
 	"#": "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": [{
@@ -157,12 +166,6 @@
 	 	"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",
@@ -172,25 +175,8 @@
 		"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",
+	"#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml",
 	"xml_out": [{
 		"CTD:restrictions": "bioml",
 		"tools": ["XTandemAdapter"]
@@ -199,8 +185,7 @@
 	"#": "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",
+	"#": "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"]
@@ -211,19 +196,10 @@
 		"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": [{
@@ -231,6 +207,7 @@
 		"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", 
@@ -244,5 +221,16 @@
 		"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"]
+	
 	}]
 }