From 85af94bc5c109f0ff375a3ff5ff7c2896ab4022b Mon Sep 17 00:00:00 2001
From: Jonathan Ott <jonathan.ott1994@gmail.com>
Date: Mon, 29 Jan 2024 12:49:32 +0100
Subject: [PATCH] fix fsx in cwl
---
runs/TurboIDSampleArc.yml | 76 ++++++++++++++++++++++
workflows/EvalTurboID/TurboIDSampleArc.cwl | 28 ++++----
2 files changed, 91 insertions(+), 13 deletions(-)
diff --git a/runs/TurboIDSampleArc.yml b/runs/TurboIDSampleArc.yml
index 87e4dae..32c4546 100644
--- a/runs/TurboIDSampleArc.yml
+++ b/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
diff --git a/workflows/EvalTurboID/TurboIDSampleArc.cwl b/workflows/EvalTurboID/TurboIDSampleArc.cwl
index 1d8690b..f79d88c 100644
--- a/workflows/EvalTurboID/TurboIDSampleArc.cwl
+++ b/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:
--
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