diff --git a/runs/FSharpArcCapsule.yml b/runs/FSharpArcCapsule.yml
index 6ecc43b77793c3fdd10abaf2a1f39e3a683a962d..2ed74490eafd4461d79886a1854ee217c1994db5 100644
--- a/runs/FSharpArcCapsule.yml
+++ b/runs/FSharpArcCapsule.yml
@@ -1,3 +1,22 @@
arcDirectory:
class: Directory
path: ../
+firstArg:
+ class: File
+ path: ../assays/measurement1/dataset/table.csv
+secondArg: ./result.csv
+
+arc:has process sequence:
+ - class: arc:process sequence
+ arc:has input:
+ - class: arc:data
+ arc:name: "./arc/assays/measurement1/dataset/table.csv"
+ arc:has output:
+ - class: arc:data
+ arc:name: "./arc/runs/fsResult1/result.csv"
+
+$namespaces:
+ arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+ - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl
diff --git a/runs/result.csv b/runs/result.csv
deleted file mode 100644
index 55137a39f41b555f9b7d26505f9c15240eec09ee..0000000000000000000000000000000000000000
--- a/runs/result.csv
+++ /dev/null
@@ -1,651 +0,0 @@
-Sum_1-2
-52.374927
-30.708113
-43.347295
-32.330910
-68.832634
-50.943254
-82.709457
-45.815823
-49.329293
-15.044567
-42.581675
-61.490285
-61.483285
-33.515325
-39.027573
-57.814962
-41.484288
-62.969456
-56.084297
-76.014723
-39.715133
-73.319637
-67.026630
-56.888570
-48.411011
-70.181930
-18.055983
-35.218257
-26.840155
-72.385753
-43.972671
-44.078586
-53.938409
-43.395488
-28.723837
-54.061480
-58.528494
-52.236839
-56.893014
-56.525366
-58.955729
-46.444395
-39.269410
-44.423325
-19.510763
-48.672524
-64.933334
-60.750569
-45.516685
-46.623334
-76.270554
-29.934011
-50.275506
-40.572500
-55.508817
-43.844585
-57.298854
-38.721723
-49.707433
-48.383707
-73.873611
-56.579798
-49.573657
-74.940937
-48.889656
-11.609634
-39.675693
-29.804500
-43.964936
-35.057027
-37.625311
-77.481503
-41.714170
-52.904955
-35.366910
-39.166247
-53.024085
-7.132227
-54.059714
-38.487312
-79.778612
-49.592970
-42.861946
-63.583801
-81.084601
-29.562834
-54.967924
-56.813437
-50.634788
-45.835761
-53.669806
-27.804082
-62.293055
-42.933661
-34.954878
-64.885836
-57.539051
-33.539328
-69.979137
-28.013399
-35.567483
-36.313160
-25.754159
-62.622885
-52.078601
-82.992087
-63.108076
-48.537387
-72.088146
-47.708756
-50.081352
-46.179143
-74.732584
-53.696995
-50.129993
-17.040583
-80.887178
-40.020833
-49.022050
-49.116439
-38.468226
-29.134830
-20.322282
-49.185777
-53.308382
-45.099085
-65.808325
-59.549146
-50.048213
-26.082749
-80.124302
-55.766722
-69.180818
-60.836923
-52.463229
-51.026135
-31.315524
-51.322238
-33.929750
-36.525866
-32.361278
-44.855573
-59.421811
-23.286046
-57.853846
-18.032623
-49.000570
-47.200617
-58.111273
-48.959961
-25.847692
-29.714310
-53.137056
-65.416045
-56.470946
-55.253781
-32.155232
-71.859925
-44.441666
-16.885794
-50.748223
-41.405682
-55.029351
-76.376410
-61.518971
-51.721628
-46.721816
-28.638947
-46.882807
-68.343571
-53.176561
-64.122778
-62.437319
-61.480298
-53.428447
-37.651474
-43.799034
-45.150540
-29.359705
-77.462318
-34.320945
-50.826392
-18.672423
-54.533843
-49.263052
-15.014251
-59.637263
-75.641556
-32.974664
-60.915148
-35.974519
-77.802002
-59.076702
-34.350295
-42.615288
-69.605218
-31.627390
-74.992208
-58.201044
-30.875197
-46.547036
-49.237101
-42.282544
-69.203356
-23.576466
-29.353965
-51.963650
-56.777796
-57.466679
-40.537154
-53.733623
-34.704655
-62.195681
-49.928415
-50.440171
-72.540199
-41.797528
-32.751826
-50.317731
-50.603325
-29.653995
-44.363277
-46.002078
-49.866360
-55.064603
-38.464424
-71.973447
-33.156272
-29.284836
-42.182426
-56.201244
-62.848672
-69.450503
-42.519988
-58.538124
-67.876770
-42.284114
-48.723362
-71.239238
-41.335381
-67.998167
-44.738949
-39.372789
-44.085337
-62.610914
-40.226752
-44.328863
-29.687844
-52.963598
-46.399305
-51.796664
-50.799966
-34.601864
-73.164871
-38.834143
-50.748055
-58.444272
-23.501147
-61.605060
-24.335268
-44.964741
-42.034866
-28.217985
-66.388532
-31.751391
-33.250285
-78.192329
-61.761701
-54.933711
-46.687613
-13.441307
-58.399611
-48.789001
-54.413686
-47.798646
-60.974053
-46.095188
-77.736080
-45.382836
-63.210533
-82.218378
-29.634936
-44.717552
-57.165995
-54.695814
-46.757029
-30.994554
-55.775549
-34.215764
-81.310734
-59.001417
-46.079728
-42.117032
-48.162080
-57.650783
-44.735961
-59.745161
-55.039142
-52.170244
-30.148709
-36.066474
-54.716652
-24.967065
-50.843673
-62.297811
-49.496099
-23.585305
-51.888732
-46.313279
-55.850779
-22.393465
-56.058621
-52.717924
-77.662074
-34.000533
-14.115106
-75.600210
-36.806491
-52.840479
-25.554121
-18.299383
-39.884859
-74.274848
-57.681610
-48.870748
-56.811627
-40.323529
-64.027898
-54.749657
-66.107093
-72.303001
-60.942526
-54.115156
-64.309181
-42.753524
-61.962672
-56.998966
-66.032093
-74.258508
-39.864467
-45.187562
-47.024809
-78.548947
-51.666372
-80.538611
-59.184048
-49.583706
-37.009837
-47.267822
-48.440376
-68.307612
-51.023075
-63.993605
-60.544180
-45.329090
-44.611970
-56.434869
-67.624087
-59.176585
-68.513906
-68.830402
-20.619566
-45.285990
-50.768093
-42.615570
-57.791240
-63.300958
-56.322222
-39.478805
-49.189127
-42.920404
-39.023948
-45.417217
-22.296066
-47.066346
-55.762485
-60.253314
-37.568683
-67.782594
-55.737468
-71.387626
-46.630654
-56.758652
-62.682231
-45.097253
-78.585691
-55.627721
-62.010825
-49.536678
-4.913428
-60.516656
-60.876080
-32.450371
-39.049506
-37.752071
-57.404212
-53.598622
-49.306831
-41.504588
-48.036989
-56.673481
-44.928617
-56.359062
-60.992957
-59.033875
-51.883007
-30.652988
-48.403692
-93.075022
-37.637492
-36.185365
-46.091212
-46.387284
-59.591843
-53.479518
-55.205289
-39.053466
-40.187032
-56.556575
-21.922778
-40.453022
-54.711698
-34.355186
-48.573944
-52.363719
-46.941065
-39.294103
-33.816825
-44.250689
-44.074156
-48.947397
-61.858121
-46.581662
-34.903942
-49.315023
-65.599510
-39.496400
-47.746650
-25.082062
-39.310162
-49.861966
-60.633814
-71.293685
-58.461712
-43.419262
-58.911596
-31.065021
-62.432397
-61.965042
-57.238112
-48.540426
-41.931047
-49.954690
-33.390882
-62.522379
-57.253377
-74.839880
-66.559072
-30.993192
-70.112733
-43.431678
-74.371371
-67.418406
-51.656030
-41.598203
-48.328989
-28.741102
-33.778325
-67.070264
-48.586437
-42.871144
-70.542905
-31.149471
-32.989862
-49.935477
-58.544938
-67.995866
-41.084719
-62.600805
-63.003809
-43.959093
-95.039498
-51.635094
-42.594618
-56.738454
-56.472886
-72.454830
-54.390798
-65.135740
-70.138773
-45.275571
-54.464354
-28.263000
-63.981719
-41.848561
-55.615102
-35.448199
-86.911426
-44.242514
-32.677179
-40.452974
-34.386452
-52.977132
-64.966342
-39.537276
-57.530906
-54.345038
-55.536818
-55.999242
-45.167076
-40.372522
-22.215040
-45.366335
-49.567678
-48.779479
-30.159274
-56.561762
-68.434903
-36.236297
-35.488041
-77.472220
-38.989784
-39.402822
-68.317668
-75.229367
-53.419890
-60.173582
-26.209845
-48.357315
-29.727833
-38.147947
-67.890142
-22.794397
-31.554084
-58.424533
-46.306834
-59.655932
-55.330720
-54.258171
-31.582894
-41.312617
-73.765279
-53.500950
-74.922643
-46.323867
-53.648006
-37.480867
-61.356103
-27.769268
-39.382548
-44.185602
-66.040173
-56.410287
-37.092155
-68.530676
-51.842190
-41.236812
-40.983752
-27.691441
-31.891113
-59.483029
-66.877746
-74.394752
-43.754073
-61.243756
-60.027122
-39.725852
-45.948957
-57.284519
-45.996091
-67.530106
-47.148547
-32.494688
-29.333068
-54.995925
-34.525909
-63.324913
-54.005796
-36.665937
-55.685400
-55.079378
-51.315077
-24.376215
-61.887355
-47.105497
-46.901127
-31.950832
-51.792501
-57.443122
-43.485227
-30.458080
-66.059519
-29.969853
-67.121573
-41.071706
-66.490999
-47.524504
-35.631804
-80.569670
-69.667320
-31.954822
-36.904120
-50.375188
-19.774263
-55.692532
-68.069211
-43.978549
-46.565912
-33.415154
-54.959587
-41.498255
-45.510471
-53.768895
-47.423433
-36.227767
-60.372391
-56.602051
-11.669908
-59.133000
-54.510422
-44.251599
-38.670563
-57.824793
-48.460889
-53.916399
-60.547234
-57.513630
-32.481570
-44.472237
-47.860284
-60.360647
-61.895478
-44.809410
-46.069994
-50.202907
-46.490782
-77.183441
-45.670381
-69.002411
-29.191174
-52.991669
-25.541652
-12.082276
-44.325765
-49.446058
-51.843428
-71.070566
-81.170712
-42.853130
-48.259251
diff --git a/workflows/ARCMount/FSharpArcCapsule.cwl b/workflows/ARCMount/FSharpArcCapsule.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..7cc7265b136c092317f4d96da299231caca83102
--- /dev/null
+++ b/workflows/ARCMount/FSharpArcCapsule.cwl
@@ -0,0 +1,74 @@
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: arc
+ entry: $(inputs.arcDirectory)
+ writable: true
+ - class: EnvVarRequirement
+ envDef:
+ - envName: DOTNET_NOLOGO
+ envValue: "true"
+ - class: NetworkAccess
+ networkAccess: true
+baseCommand: [dotnet, fsi, "./arc/workflows/ARCMount/script.fsx"]
+inputs:
+ arcDirectory:
+ type: Directory
+outputs:
+ output:
+ type: File
+ outputBinding:
+ glob: "./arc/runs/fsResult1/result.csv"
+
+arc:has technology type:
+ - class: arc:technology type
+ arc:annotation value: "Docker Container"
+
+arc:technology platform: ".NET"
+
+arc:performer:
+ - class: arc:Person
+ arc:first name: "Timo"
+ arc:last name: "Mühlhaus"
+ arc:email: "muehlhaus@bio.uni-kl.de "
+ arc:affiliation: "RPTU Kaiserslautern/Landau"
+ arc:has role:
+ - class: arc:role
+ arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/"
+ arc:annotation value: "Formal analysis"
+
+arc:has process sequence:
+ - class: arc:process sequence
+ arc:name: "script.fsx"
+ arc:has input:
+ - class: arc:data
+ arc:name: "./arc/assays/measurement1/dataset/table.csv"
+ arc:has output:
+ - class: arc:data
+ arc:name: "./arc/runs/fsResult1/result.csv"
+ arc:has parameter value:
+ - class: arc:process parameter value
+ arc:has parameter:
+ - class: arc:protocol parameter
+ arc:has parameter name:
+ - class: arc:parameter name
+ arc:term accession: "http://purl.obolibrary.org/obo/NCIT_C43582"
+ arc:term source REF: "NCIT"
+ arc:annotation value: "Data Transformation"
+ arc:value:
+ - class: arc:ontology annotation
+ arc:term accession: "http://purl.obolibrary.org/obo/NCIT_C64911"
+ arc:term source REF: "NCIT"
+ arc:annotation value: "Addition"
+
+
+$namespaces:
+ arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+ - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl
\ No newline at end of file
diff --git a/workflows/FSharpArcCapsule/script.fsx b/workflows/ARCMount/script.fsx
similarity index 100%
rename from workflows/FSharpArcCapsule/script.fsx
rename to workflows/ARCMount/script.fsx
diff --git a/workflows/.gitkeep b/workflows/Devcontainer/.gitkeep
similarity index 100%
rename from workflows/.gitkeep
rename to workflows/Devcontainer/.gitkeep
diff --git a/workflows/Devcontainer/FSharpArcCapsule.cwl b/workflows/Devcontainer/FSharpArcCapsule.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..d3f80bc08d2146b1143b14c542f1b8f95ea029b3
--- /dev/null
+++ b/workflows/Devcontainer/FSharpArcCapsule.cwl
@@ -0,0 +1,75 @@
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerImageId: "devcontainer"
+ dockerFile: {$include: "FSharpArcCapsule/Dockerfile"}
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: arc
+ entry: $(inputs.arcDirectory)
+ writable: true
+ - class: EnvVarRequirement
+ envDef:
+ - envName: DOTNET_NOLOGO
+ envValue: "true"
+ - class: NetworkAccess
+ networkAccess: true
+baseCommand: [dotnet, fsi, "./arc/workflows/Devcontainer/FSharpArcCapsule/script.fsx"]
+inputs:
+ arcDirectory:
+ type: Directory
+outputs:
+ output:
+ type: File
+ outputBinding:
+ glob: "./arc/runs/fsResult1/result.csv"
+
+arc:has technology type:
+ - class: arc:technology type
+ arc:annotation value: "Fsharp Devcontainer"
+
+arc:technology platform: ".NET"
+
+arc:performer:
+ - class: arc:Person
+ arc:first name: "Timo"
+ arc:last name: "Mühlhaus"
+ arc:email: "muehlhaus@bio.uni-kl.de "
+ arc:affiliation: "RPTU Kaiserslautern/Landau"
+ arc:has role:
+ - class: arc:role
+ arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/"
+ arc:annotation value: "Formal analysis"
+
+arc:has process sequence:
+ - class: arc:process sequence
+ arc:name: "script.fsx"
+ arc:has input:
+ - class: arc:data
+ arc:name: "./arc/assays/measurement1/dataset/table.csv"
+ arc:has output:
+ - class: arc:data
+ arc:name: "./arc/runs/fsResult1/result.csv"
+ arc:has parameter value:
+ - class: arc:process parameter value
+ arc:has parameter:
+ - class: arc:protocol parameter
+ arc:has parameter name:
+ - class: arc:parameter name
+ arc:term accession: "http://purl.obolibrary.org/obo/NCIT_C43582"
+ arc:term source REF: "NCIT"
+ arc:annotation value: "Data Transformation"
+ arc:value:
+ - class: arc:ontology annotation
+ arc:term accession: "http://purl.obolibrary.org/obo/NCIT_C64911"
+ arc:term source REF: "NCIT"
+ arc:annotation value: "Addition"
+
+
+$namespaces:
+ arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+ - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl
\ No newline at end of file
diff --git a/workflows/FSharpArcCapsule/.config/dotnet-tools.json b/workflows/Devcontainer/FSharpArcCapsule/.config/dotnet-tools.json
similarity index 100%
rename from workflows/FSharpArcCapsule/.config/dotnet-tools.json
rename to workflows/Devcontainer/FSharpArcCapsule/.config/dotnet-tools.json
diff --git a/workflows/FSharpArcCapsule/.devcontainer/devcontainer.json b/workflows/Devcontainer/FSharpArcCapsule/.devcontainer/devcontainer.json
similarity index 100%
rename from workflows/FSharpArcCapsule/.devcontainer/devcontainer.json
rename to workflows/Devcontainer/FSharpArcCapsule/.devcontainer/devcontainer.json
diff --git a/workflows/FSharpArcCapsule/.devcontainer/settings.vscode.json b/workflows/Devcontainer/FSharpArcCapsule/.devcontainer/settings.vscode.json
similarity index 100%
rename from workflows/FSharpArcCapsule/.devcontainer/settings.vscode.json
rename to workflows/Devcontainer/FSharpArcCapsule/.devcontainer/settings.vscode.json
diff --git a/workflows/FSharpArcCapsule/Dockerfile b/workflows/Devcontainer/FSharpArcCapsule/Dockerfile
similarity index 100%
rename from workflows/FSharpArcCapsule/Dockerfile
rename to workflows/Devcontainer/FSharpArcCapsule/Dockerfile
diff --git a/workflows/Devcontainer/FSharpArcCapsule/script.fsx b/workflows/Devcontainer/FSharpArcCapsule/script.fsx
new file mode 100644
index 0000000000000000000000000000000000000000..155693f823fcdcccff9a5ac13dca26566792945d
--- /dev/null
+++ b/workflows/Devcontainer/FSharpArcCapsule/script.fsx
@@ -0,0 +1,20 @@
+#r "nuget: FSharp.Data, 5.0.2"
+
+open FSharp.Data
+open System.IO
+
+printfn "%A" (System.IO.Directory.GetCurrentDirectory())
+
+let data =
+ CsvFile
+ .Load(Path.Combine(System.IO.Directory.GetCurrentDirectory(),"./arc/assays/measurement1/dataset/table.csv"))
+ .Cache()
+
+let r =
+ [
+ yield "Sum_1-2"
+ for row in data.Rows do
+ yield sprintf "%f" ((row.["value_1"].AsFloat()) + (row.["value_2"].AsFloat()))
+ ]
+
+System.IO.File.WriteAllLines("./arc/runs/fsResult1/result.csv",r)
\ No newline at end of file
diff --git a/workflows/FSharpArcCapsule.cwl b/workflows/FSharpArcCapsule.cwl
deleted file mode 100644
index f3aa1c3f95a5738b6ef96e0dfa546651bc739c0c..0000000000000000000000000000000000000000
--- a/workflows/FSharpArcCapsule.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-cwlVersion: v1.2
-class: CommandLineTool
-hints:
- DockerRequirement:
- dockerImageId: "devcontainer"
- dockerFile: {$include: "FSharpArcCapsule/Dockerfile"}
-requirements:
- - class: InitialWorkDirRequirement
- listing:
- - entryname: arc
- entry: $(inputs.arcDirectory)
- writable: true
- - class: EnvVarRequirement
- envDef:
- - envName: DOTNET_NOLOGO
- envValue: "true"
- - envName: CWL
- envValue: "true"
- - class: NetworkAccess
- networkAccess: true
-baseCommand: [dotnet, fsi, "./arc/workflows/FSharpArcCapsule/script.fsx"]
-inputs:
- arcDirectory:
- type: Directory
-outputs:
- output:
- type: File
- outputBinding:
- glob: "./arc/runs/fsResult1/result.csv"
\ No newline at end of file
diff --git a/workflows/FixedScript/FSharpArcCapsule.cwl b/workflows/FixedScript/FSharpArcCapsule.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..aa0b5e02141bebb3b299403b52c8a69d919f5095
--- /dev/null
+++ b/workflows/FixedScript/FSharpArcCapsule.cwl
@@ -0,0 +1,75 @@
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: script.fsx
+ entry:
+ $include: script.fsx
+ - class: EnvVarRequirement
+ envDef:
+ - envName: DOTNET_NOLOGO
+ envValue: "true"
+ - class: NetworkAccess
+ networkAccess: true
+baseCommand: [dotnet, fsi, script.fsx]
+inputs:
+ firstArg:
+ type: File
+ inputBinding:
+ position: 1
+ secondArg:
+ type: string
+ inputBinding:
+ position: 2
+
+outputs:
+ output:
+ type: File
+ outputBinding:
+ glob: "*.csv"
+
+arc:has technology type:
+ - class: arc:technology type
+ arc:annotation value: "Docker Container"
+
+arc:technology platform: ".NET"
+
+arc:performer:
+ - class: arc:Person
+ arc:first name: "Timo"
+ arc:last name: "Mühlhaus"
+ arc:email: "muehlhaus@bio.uni-kl.de "
+ arc:affiliation: "RPTU Kaiserslautern/Landau"
+ arc:has role:
+ - class: arc:role
+ arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/"
+ arc:annotation value: "Formal analysis"
+
+arc:has process sequence:
+ - class: arc:process sequence
+ arc:name: "script.fsx"
+ arc:has parameter value:
+ - class: arc:process parameter value
+ arc:has parameter:
+ - class: arc:protocol parameter
+ arc:has parameter name:
+ - class: arc:parameter name
+ arc:term accession: "http://purl.obolibrary.org/obo/NCIT_C43582"
+ arc:term source REF: "NCIT"
+ arc:annotation value: "Data Transformation"
+ arc:value:
+ - class: arc:ontology annotation
+ arc:term accession: "http://purl.obolibrary.org/obo/NCIT_C64911"
+ arc:term source REF: "NCIT"
+ arc:annotation value: "Addition"
+
+
+$namespaces:
+ arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+ - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl
\ No newline at end of file
diff --git a/workflows/FixedScript/script.fsx b/workflows/FixedScript/script.fsx
new file mode 100644
index 0000000000000000000000000000000000000000..581145dd3da657009c1e3c087cd95d756a9cc178
--- /dev/null
+++ b/workflows/FixedScript/script.fsx
@@ -0,0 +1,22 @@
+#r "nuget: FSharp.Data, 5.0.2"
+
+open FSharp.Data
+open System.IO
+
+let args : string array = fsi.CommandLineArgs |> Array.tail
+let first = args.[0]
+let second = args.[1]
+
+let data =
+ CsvFile
+ .Load(first)
+ .Cache()
+
+let r =
+ [
+ yield "Sum_1-2"
+ for row in data.Rows do
+ yield sprintf "%f" ((row.["value_1"].AsFloat()) + (row.["value_2"].AsFloat()))
+ ]
+
+System.IO.File.WriteAllLines(second,r)
\ No newline at end of file