fix fsx in cwl

runs/TurboIDSampleArc.yml

@@ -11,3 +11,79 @@ input:
   class: File
   path: ../assays/MSEval/dataset/TEF_PSBQ_LON_MS264DDAfs_combined_protein.tsv
 runID: test
+
+
+arc:has measurement type:
+  - class: arc:measurement type
+    arc:term accession: "http://purl.obolibrary.org/obo/OMIT_0023015"
+    arc:term source REF: "OMIT"
+    arc:annotation value: "Proteomics"
+    
+
+arc:has technology type:
+  - class: arc:technology type
+    arc:term accession: "http://purl.obolibrary.org/obo/OMIT_0013943"
+    arc:term source REF: "OMIT"
+    arc:annotation value: "Mass Spectrometry"
+
+arc:technology platform: SCIEX
+
+arc:performer:
+  - class: arc:Person
+    arc:first name: "David"
+    arc:last name: "Zimmer"
+    arc:email: "d_zimmer@rptu.de"
+    arc:affiliation: "RPTU Kaiserslautern/Landau"
+    arc:has role: 
+      - class: arc:role
+        arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/"
+        arc:annotation value: "Formal analysis"
+
+arc:has process sequence:
+  - class: arc:process sequence
+    arc:name: "MassSpectrometry"
+    arc:has input: 
+      - class: arc:sample
+        arc:name: "PR135_01"
+      - class: arc:sample
+        arc:name: "PR135_02"
+    arc:has output:
+      - class: arc:data
+        arc:name: "20220531TRR3R135001"
+      - class: arc:data
+        arc:name: "20220531TRR3R135003"
+    arc:has parameter value: 
+      - class: arc:process parameter value
+        arc:has parameter:
+          - class: arc:protocol parameter
+            arc:has parameter name: 
+            - class: arc:parameter name
+              arc:term accession: "http://purl.obolibrary.org/obo/PATO_0000146"
+              arc:term source REF: "PATO"
+              arc:annotation value: "temperature"
+        arc:has unit:
+          - class: arc:unit
+            arc:term accession: "http://purl.obolibrary.org/obo/UO_0000027"
+            arc:term source REF: "UO"
+            arc:annotation value: "degree Celsius"
+        arc:value: 35
+      - class: arc:process parameter value
+        arc:has parameter:
+          - class: arc:protocol parameter
+            arc:has parameter name: 
+            - class: arc:parameter name
+              arc:term accession: "http://purl.obolibrary.org/obo/OBI_0000615"
+              arc:term source REF: "OBI"
+              arc:annotation value: "protein expression profiling assay"
+        arc:value: 
+          - class: arc:ontology annotation
+            arc:term accession: "http://purl.obolibrary.org/obo/BAO_0010027"
+            arc:term source REF: "BAO"
+            arc:annotation value: "shotgun MS protein profiling assay"
+
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl

workflows/EvalTurboID/TurboIDSampleArc.cwl

@@ -5,41 +5,43 @@ hints:
     dockerPull: mcr.microsoft.com/dotnet/sdk:7.0
 requirements:
   # - class: InlineJavascriptRequirement
-  # - class: InitialWorkDirRequirement
-  #   listing:
-  #     - entry: $(inputs.scriptDirectory)
-  #       writable: true
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: EvalTurboID.fsx
+        entry:
+          $include: EvalTurboID.fsx
+
   - class: EnvVarRequirement
     envDef:
       - envName: DOTNET_NOLOGO
         envValue: "true"
   - class: NetworkAccess
     networkAccess: true
-baseCommand: [dotnet, fsi]
+baseCommand: [dotnet, fsi, EvalTurboID.fsx]
 inputs:
-  scriptFile:
-    type: File
-    inputBinding:
-      position: 1
+  # scriptFile:
+  #   type: File
+  #   inputBinding:
+  #     position: 1
   input:
     type: File
     inputBinding:
-      position: 2
+      position: 1
       prefix: -i
   mappingFile:
     type: File
     inputBinding:
-      position: 3
+      position: 2
       prefix: -m
   arcDirectory:
     type: Directory
     inputBinding:
-      position: 4
+      position: 3
       prefix: -a
   runID:
     type: string
     inputBinding:
-      position: 5
+      position: 4
       prefix: -id
 outputs:
   output: