diff --git a/assays/Growth/isa.assay.xlsx b/assays/Growth/isa.assay.xlsx deleted file mode 100644 index 880743d05fac1dc80b6927ab8874035bbab01d64..0000000000000000000000000000000000000000 Binary files a/assays/Growth/isa.assay.xlsx and /dev/null differ diff --git a/assays/Metabolomics/isa.assay.xlsx b/assays/Metabolomics/isa.assay.xlsx deleted file mode 100644 index 7ea17a49da2abed5dec6b4373c55e2ebf7cbcfd0..0000000000000000000000000000000000000000 Binary files a/assays/Metabolomics/isa.assay.xlsx and /dev/null differ diff --git a/assays/Metabolomics/protocols/.gitkeep b/assays/Metabolomics/protocols/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/Proteomics/isa.assay.xlsx b/assays/Proteomics/isa.assay.xlsx index 3d06cda6f4a14e62f695001953ead0bb7a145943..504f6b611df17e12835be08d761fc69ee4ac2e1f 100644 Binary files a/assays/Proteomics/isa.assay.xlsx and b/assays/Proteomics/isa.assay.xlsx differ diff --git a/assays/Proteomics/isa.datamap.xlsx b/assays/Proteomics/isa.datamap.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..7b84772f7cd49d3e65dec7bcf23809fe917539b8 Binary files /dev/null and b/assays/Proteomics/isa.datamap.xlsx differ diff --git a/assays/Transcriptomics/isa.assay.xlsx b/assays/Transcriptomics/isa.assay.xlsx index 662a8b99a8d9fecca4a772cc72fa5664a3b6cde1..24f0a56205e8c20b78d9d158f1ab1e102bf74455 100644 Binary files a/assays/Transcriptomics/isa.assay.xlsx and b/assays/Transcriptomics/isa.assay.xlsx differ diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index 8d97da9b53368b4e6fdbc9f619ee9d1399cb038c..ba82dfb4201b6b95f1066b49a290e5587b705f0c 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/assays/Growth/README.md b/runs/Proteomics/ProteomicsStatistics.fsx similarity index 100% rename from assays/Growth/README.md rename to runs/Proteomics/ProteomicsStatistics.fsx diff --git a/runs/Proteomics/run.cwl b/runs/Proteomics/run.cwl new file mode 100644 index 0000000000000000000000000000000000000000..1e8bd93f9f980e9fed3f66151ff73207aa370464 --- /dev/null +++ b/runs/Proteomics/run.cwl @@ -0,0 +1,61 @@ +cwlVersion: v1.2 +class: CommandLineTool +hints: + DockerRequirement: + dockerPull: mcr.microsoft.com/dotnet/sdk:6.0 +requirements: + - class: InitialWorkDirRequirement + listing: + - entryname: ProteomicsStatistics.fsx + entry: + $include: ProteomicsStatistics.fsx + - class: EnvVarRequirement + envDef: + - envName: DOTNET_NOLOGO + envValue: "true" + - class: NetworkAccess + networkAccess: true +baseCommand: [dotnet, fsi, ProteomicsStatistics.fsx] + +outputs: + output: + type: File + outputBinding: + glob: "imputeKnnNoLow_35.txt" + output: + type: File + outputBinding: + glob: "imputeKnnNoLow_40.txt" + output: + type: File + outputBinding: + glob: "protein35zScores.txt" + output: + type: File + outputBinding: + glob: "protein40zScores.txt" + + +arc:has technology type: + - class: arc:technology type + arc:annotation value: "Docker Container" + +arc:technology platform: ".NET" + +arc:performer: + - class: arc:Person + arc:first name: "Benedikt" + arc:last name: "Venn" + arc:email: "venn@bio.uni-kl.de" + arc:affiliation: "TU Kaiserslautern" + arc:has role: + - class: arc:role + arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/" + arc:annotation value: "Formal analysis" + + +$namespaces: + arc: https://github.com/nfdi4plants/ARC_ontology + +$schemas: + - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl diff --git a/assays/Growth/dataset/.gitkeep b/runs/Transcriptomics/TranscriptomicsStatistics.fsx similarity index 100% rename from assays/Growth/dataset/.gitkeep rename to runs/Transcriptomics/TranscriptomicsStatistics.fsx diff --git a/runs/Transcriptomics/run.cwl b/runs/Transcriptomics/run.cwl new file mode 100644 index 0000000000000000000000000000000000000000..61f61a252171f5cb1a911e57ea5aa4cc4712c014 --- /dev/null +++ b/runs/Transcriptomics/run.cwl @@ -0,0 +1,61 @@ +cwlVersion: v1.2 +class: CommandLineTool +hints: + DockerRequirement: + dockerPull: mcr.microsoft.com/dotnet/sdk:6.0 +requirements: + - class: InitialWorkDirRequirement + listing: + - entryname: TranscriptomicsStatistics.fsx + entry: + $include: TranscriptomicsStatistics.fsx + - class: EnvVarRequirement + envDef: + - envName: DOTNET_NOLOGO + envValue: "true" + - class: NetworkAccess + networkAccess: true +baseCommand: [dotnet, fsi, TranscriptomicsStatistics.fsx] + +outputs: + output: + type: File + outputBinding: + glob: "2019_11_12_TPM_normalized_RNAseq_counts.csv" + output: + type: File + outputBinding: + glob: "2020_01_29_DEX_T1intercept_noCoV_multipletestingcorrected_added0_01_differencecutoff.csv" + output: + type: File + outputBinding: + glob: "protein35zScores.txt" + output: + type: File + outputBinding: + glob: "protein40zScores.txt" + + +arc:has technology type: + - class: arc:technology type + arc:annotation value: "Docker Container" + +arc:technology platform: ".NET" + +arc:performer: + - class: arc:Person + arc:first name: "Benedikt" + arc:last name: "Venn" + arc:email: "venn@bio.uni-kl.de" + arc:affiliation: "TU Kaiserslautern" + arc:has role: + - class: arc:role + arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/" + arc:annotation value: "Formal analysis" + + +$namespaces: + arc: https://github.com/nfdi4plants/ARC_ontology + +$schemas: + - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl diff --git a/assays/Metabolomics/README.md b/studies/Growth/README.md similarity index 100% rename from assays/Metabolomics/README.md rename to studies/Growth/README.md diff --git a/studies/Growth/isa.study.xlsx b/studies/Growth/isa.study.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..62c0e16e80db405cee94876e6b575017ef39cfd3 Binary files /dev/null and b/studies/Growth/isa.study.xlsx differ diff --git a/assays/Growth/protocols/.gitkeep b/studies/Growth/protocols/.gitkeep similarity index 100% rename from assays/Growth/protocols/.gitkeep rename to studies/Growth/protocols/.gitkeep diff --git a/studies/HeatstressExperiment/protocols/2022-07-12_121059.png b/studies/Growth/protocols/2022-07-12_121059.png similarity index 100% rename from studies/HeatstressExperiment/protocols/2022-07-12_121059.png rename to studies/Growth/protocols/2022-07-12_121059.png diff --git a/assays/Metabolomics/dataset/.gitkeep b/studies/Growth/resources/.gitkeep similarity index 100% rename from assays/Metabolomics/dataset/.gitkeep rename to studies/Growth/resources/.gitkeep diff --git a/studies/HeatstressExperiment/README.md b/studies/HeatstressExperiment/README.md deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/studies/HeatstressExperiment/isa.study.xlsx b/studies/HeatstressExperiment/isa.study.xlsx deleted file mode 100644 index 4206bb4be627c7f751ecf5a83281f92d0a6850fd..0000000000000000000000000000000000000000 Binary files a/studies/HeatstressExperiment/isa.study.xlsx and /dev/null differ diff --git a/studies/HeatstressExperiment/protocols/.gitkeep b/studies/HeatstressExperiment/protocols/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/studies/HeatstressExperiment/resources/.gitkeep b/studies/HeatstressExperiment/resources/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000