From 0e7c9ab74d05990cee2097bfecbfd1caa79f153c Mon Sep 17 00:00:00 2001
From: Manuel Feser <feser@ipk-gatersleben.de>
Date: Thu, 5 Sep 2024 09:52:54 +0100
Subject: [PATCH] Imported barley-trial setup data
---
assays/with-observation-units/isa.assay.xlsx | Bin 0 -> 8699 bytes
.../without-observation-units/isa.assay.xlsx | Bin 0 -> 8763 bytes
assays/yourAssayName/README.md | 0
assays/yourAssayName/dataset/.gitkeep | 0
assays/yourAssayName/dataset/README.md | 5 --
assays/yourAssayName/isa.assay.xlsx | Bin 2656 -> 0 bytes
assays/yourAssayName/isa.datapackage.xlsx | Bin 10400 -> 0 bytes
assays/yourAssayName/protocols/.gitkeep | 0
assays/yourAssayName/protocols/README.md | 5 --
isa.investigation.xlsx | Bin 3251 -> 11018 bytes
metadata.json | 1 +
runs/yourRunName.cwl | 15 -----
runs/yourRunName.yml | 5 --
runs/yourRunResultName/README.md | 6 --
runs/yourRunResultName/plot1.html | 61 ------------------
studies/with-observation-units/isa.study.xlsx | Bin 0 -> 23134 bytes
studies/with-observation-units/tdf.tsv | 6 ++
.../without-observation-units/isa.study.xlsx | Bin 0 -> 14896 bytes
studies/without-observation-units/tdf.tsv | 6 ++
studies/yourStudyName/README.md | 0
studies/yourStudyName/isa.study.xlsx | Bin 3129 -> 0 bytes
studies/yourStudyName/protocols/.gitkeep | 0
studies/yourStudyName/protocols/README.md | 5 --
studies/yourStudyName/resources/.gitkeep | 0
studies/yourStudyName/resources/README.md | 5 --
workflows/yourWorkflowName/README.md | 5 --
26 files changed, 13 insertions(+), 112 deletions(-)
create mode 100644 assays/with-observation-units/isa.assay.xlsx
create mode 100644 assays/without-observation-units/isa.assay.xlsx
delete mode 100644 assays/yourAssayName/README.md
delete mode 100644 assays/yourAssayName/dataset/.gitkeep
delete mode 100644 assays/yourAssayName/dataset/README.md
delete mode 100644 assays/yourAssayName/isa.assay.xlsx
delete mode 100644 assays/yourAssayName/isa.datapackage.xlsx
delete mode 100644 assays/yourAssayName/protocols/.gitkeep
delete mode 100644 assays/yourAssayName/protocols/README.md
create mode 100644 metadata.json
delete mode 100644 runs/yourRunName.cwl
delete mode 100644 runs/yourRunName.yml
delete mode 100644 runs/yourRunResultName/README.md
delete mode 100644 runs/yourRunResultName/plot1.html
create mode 100644 studies/with-observation-units/isa.study.xlsx
create mode 100644 studies/with-observation-units/tdf.tsv
create mode 100644 studies/without-observation-units/isa.study.xlsx
create mode 100644 studies/without-observation-units/tdf.tsv
delete mode 100644 studies/yourStudyName/README.md
delete mode 100644 studies/yourStudyName/isa.study.xlsx
delete mode 100644 studies/yourStudyName/protocols/.gitkeep
delete mode 100644 studies/yourStudyName/protocols/README.md
delete mode 100644 studies/yourStudyName/resources/.gitkeep
delete mode 100644 studies/yourStudyName/resources/README.md
delete mode 100644 workflows/yourWorkflowName/README.md
diff --git a/assays/with-observation-units/isa.assay.xlsx b/assays/with-observation-units/isa.assay.xlsx
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diff --git a/assays/without-observation-units/isa.assay.xlsx b/assays/without-observation-units/isa.assay.xlsx
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diff --git a/assays/yourAssayName/README.md b/assays/yourAssayName/README.md
deleted file mode 100644
index e69de29..0000000
diff --git a/assays/yourAssayName/dataset/.gitkeep b/assays/yourAssayName/dataset/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/assays/yourAssayName/dataset/README.md b/assays/yourAssayName/dataset/README.md
deleted file mode 100644
index b071a7c..0000000
--- a/assays/yourAssayName/dataset/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-## ARCs
-### Assays
-
-`/assays/<yourAssayName>/dataset`
-: assay dataset
diff --git a/assays/yourAssayName/isa.assay.xlsx b/assays/yourAssayName/isa.assay.xlsx
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diff --git a/assays/yourAssayName/protocols/.gitkeep b/assays/yourAssayName/protocols/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/assays/yourAssayName/protocols/README.md b/assays/yourAssayName/protocols/README.md
deleted file mode 100644
index 7525c30..0000000
--- a/assays/yourAssayName/protocols/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-## ARCs
-### Assays
-
-`/assays/<yourAssayName>/protocols`
-: assay protocol as text (e.g SOP)
diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
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diff --git a/runs/yourRunName.cwl b/runs/yourRunName.cwl
deleted file mode 100644
index 08f52dd..0000000
--- a/runs/yourRunName.cwl
+++ /dev/null
@@ -1,15 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: [fsi.exe, /…/workflows/FSharpCodespace/script1.fsx]
-inputs:
- inputFiles:
- type:
- type: array
- items: string
- inputBinding:
- position: 1
-outputs:
- plotted_data:
- type: File
- outputBinding:
- glob: $(inputs.plot)
diff --git a/runs/yourRunName.yml b/runs/yourRunName.yml
deleted file mode 100644
index c095540..0000000
--- a/runs/yourRunName.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-inputFiles:
- - /…/assays/yourAssay/dataset/Sample1.txt
- - /…/assays/yourAssay/dataset/Sample2.dat
- - /…/assays/yourAssay/dataset/Sample3.txt
-plot: ./yourRunResultName/plot1.html
diff --git a/runs/yourRunResultName/README.md b/runs/yourRunResultName/README.md
deleted file mode 100644
index 9991f93..0000000
--- a/runs/yourRunResultName/README.md
+++ /dev/null
@@ -1,6 +0,0 @@
-# ARCs
-
-## ARC directory structure
-
-`./runs/<yourRunResultName>`
-: folder for results of your run aka. workflow execution
diff --git a/runs/yourRunResultName/plot1.html b/runs/yourRunResultName/plot1.html
deleted file mode 100644
index 0c76f57..0000000
--- a/runs/yourRunResultName/plot1.html
+++ /dev/null
@@ -1,61 +0,0 @@
-
-<!DOCTYPE html>
-<html>
- <head>
- <!-- Plotly.js -->
- <meta http-equiv="X-UA-Compatible" content="IE=11" >
- <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
- <style>
- .container {
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- padding-left: 25px;
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- @media (min-width: 768px) {
- .container {
- width: 750px;
- }
- }
- @media (min-width: 992px) {
- .container {
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- @media (min-width: 1200px) {
- .container {
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- </style>
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- <body>
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-
- var renderPlotly = function() {
- var fsharpPlotlyRequire = requirejs.config({context:'fsharp-plotly',paths:{plotly:'https://cdn.plot.ly/plotly-latest.min'}});
- fsharpPlotlyRequire(['plotly'], function(Plotly) {
-
- var data = [{"type":"scatter","x":[1.0],"y":[2.0],"mode":"markers","marker":{}}];
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- var config = {};
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- };
- if ((typeof(requirejs) !== typeof(Function)) || (typeof(requirejs.config) !== typeof(Function))) {
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HcmV?d00001
diff --git a/studies/with-observation-units/tdf.tsv b/studies/with-observation-units/tdf.tsv
new file mode 100644
index 0000000..1006f8e
--- /dev/null
+++ b/studies/with-observation-units/tdf.tsv
@@ -0,0 +1,6 @@
+Variable ID Variable Name Variable Accession Number Trait Trait Accession Number Method Method Accession Number Method Description Scale Scale Accession Number Scale Type Scale Values
+AwnTip_M_date Awn tipping Awn tipping Measurement Record the date when 50% of the awns have tipped Date Date
+Head_M_date Heading Heading Measurement Record date when 50% of the heads have emerged Date Date
+Mat_M_date Maturity Maturity Measurement Record date when 50% of the heads have matured Date Date
+PlntHght_M_cm Plant height Plant height Measurement Record the height of the plant in centimeters cm Numerical
+RwTyp_E_1to2 Row type Row type Estimation Score the row type of the plant 1to2 Nominal 2:2-rowed;6:6-rowed
\ No newline at end of file
diff --git a/studies/without-observation-units/isa.study.xlsx b/studies/without-observation-units/isa.study.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..c4a64f2e229bad136dddb9eeb12e5a303d022fb6
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diff --git a/studies/without-observation-units/tdf.tsv b/studies/without-observation-units/tdf.tsv
new file mode 100644
index 0000000..1006f8e
--- /dev/null
+++ b/studies/without-observation-units/tdf.tsv
@@ -0,0 +1,6 @@
+Variable ID Variable Name Variable Accession Number Trait Trait Accession Number Method Method Accession Number Method Description Scale Scale Accession Number Scale Type Scale Values
+AwnTip_M_date Awn tipping Awn tipping Measurement Record the date when 50% of the awns have tipped Date Date
+Head_M_date Heading Heading Measurement Record date when 50% of the heads have emerged Date Date
+Mat_M_date Maturity Maturity Measurement Record date when 50% of the heads have matured Date Date
+PlntHght_M_cm Plant height Plant height Measurement Record the height of the plant in centimeters cm Numerical
+RwTyp_E_1to2 Row type Row type Estimation Score the row type of the plant 1to2 Nominal 2:2-rowed;6:6-rowed
\ No newline at end of file
diff --git a/studies/yourStudyName/README.md b/studies/yourStudyName/README.md
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diff --git a/studies/yourStudyName/protocols/.gitkeep b/studies/yourStudyName/protocols/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/studies/yourStudyName/protocols/README.md b/studies/yourStudyName/protocols/README.md
deleted file mode 100644
index 68f066e..0000000
--- a/studies/yourStudyName/protocols/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-## ARCs
-### Studies
-
-`/studies/<yourStudyName>/protocols`
-: study protocol as text
diff --git a/studies/yourStudyName/resources/.gitkeep b/studies/yourStudyName/resources/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/studies/yourStudyName/resources/README.md b/studies/yourStudyName/resources/README.md
deleted file mode 100644
index 497860e..0000000
--- a/studies/yourStudyName/resources/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-## ARCs
-### Studies
-
-`/studies/<yourStudyName>/resources`
-: your resources (input materials, external data)
diff --git a/workflows/yourWorkflowName/README.md b/workflows/yourWorkflowName/README.md
deleted file mode 100644
index 40e7fdf..0000000
--- a/workflows/yourWorkflowName/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-## ARC directory structure
-
-### workflows (aka. codespace, code, code capsules, codecaps)
-
-All programmatic components of an ARC should go here, in the form of code and environment.
--
GitLab