From f0587d1222919470bf8b0b1b8d936794a22f3088 Mon Sep 17 00:00:00 2001
From: Edmore Moyo <etmoyo@gmail.com>
Date: Thu, 17 Apr 2025 11:15:29 -0400
Subject: [PATCH 1/2] defining initial datatypes for input and output

---
 .gitignore  |  3 ++-
 README.md   | 25 +++++++++++++++++++++++++
 config.json |  6 ++++++
 input.json  | 13 +++++++++++++
 output.json | 13 +++++++++++++
 5 files changed, 59 insertions(+), 1 deletion(-)
 create mode 100644 config.json
 create mode 100644 input.json
 create mode 100644 output.json

diff --git a/.gitignore b/.gitignore
index 6320cd2..7106392 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
-data
\ No newline at end of file
+data
+.DS_Store
diff --git a/README.md b/README.md
index cad16e8..3109864 100644
--- a/README.md
+++ b/README.md
@@ -16,3 +16,28 @@ To test, create `input` and `output` subfolders in the `data` directory. Create
 Re-Run: `docker-compose up --build`
 
 The testfile should be copied to the `data/output` directory.
+
+
+Read all input parameters from a config.json file. config.json is created by brainlife.io at runtime on the current working directory.
+Read all input data from paths specified in config.json (config.json contains both the input parameters; such as command line arguments as well as paths to data files; like t1.nii.gz)
+Write all output files in the current directory (./), in a structure defined as a Brainlife datatype. More information about Brainlife datatypes.
+
+App Development Timeline
+You would normally follow these steps to develop and register your App on Brainlife.
+
+Develop an algorithm that runs on your laptop or local cluster with your test datasets.
+Create a sample config.json file.
+Create main that parses config.json and passes it to your algorithm.
+Publish it as public github repo.
+Register your App on Brainlife. During this step, you can define what parameters and input file(s) should be made available to your App via config.json.
+Contact resource administrators and ask them to enable your App (more below).
+
+examples:
+https://github.com/BrainlifeMEEG/app-ICA-apply/tree/master
+Datatype: https://brainlife.io/app/63358285db978c7991a30e5b
+
+References:
+https://github.com/brainlife/abcd-spec
+https://brainlife.io/docs/apps/introduction/
+https://brainlife.io/docs/user/datatypes/
+https://brainlife.io/docs/apps/register/
diff --git a/config.json b/config.json
new file mode 100644
index 0000000..2fd1b34
--- /dev/null
+++ b/config.json
@@ -0,0 +1,6 @@
+[
+    {
+        "numCores": 1,
+        "type": "int"
+    }
+]
\ No newline at end of file
diff --git a/input.json b/input.json
new file mode 100644
index 0000000..8aa0fe0
--- /dev/null
+++ b/input.json
@@ -0,0 +1,13 @@
+{
+    "name" : "echo/input",
+    "desc" : "echo input",
+    "files" : [
+        {
+            "id" : "fcs",
+            "filename" : "input.fcs",
+            "desc" : "fcs file",
+            "ext" : ".fcs",
+            "required" : true
+        }
+    ]
+}
\ No newline at end of file
diff --git a/output.json b/output.json
new file mode 100644
index 0000000..07e2cb5
--- /dev/null
+++ b/output.json
@@ -0,0 +1,13 @@
+{
+    "name" : "echo/output",
+    "desc" : "echo output",
+    "files" : [
+        {
+            "id" : "fcs",
+            "filename" : "output.csv",
+            "desc" : "csv file",
+            "ext" : ".csv",
+            "required" : true
+        }
+    ]
+}
\ No newline at end of file

From f8c79767057e54c487c957804ed643e5e66788d7 Mon Sep 17 00:00:00 2001
From: Edmore Moyo <etmoyo@gmail.com>
Date: Thu, 17 Apr 2025 11:18:06 -0400
Subject: [PATCH 2/2] updates README

---
 README.md | 25 -------------------------
 1 file changed, 25 deletions(-)

diff --git a/README.md b/README.md
index 3109864..cad16e8 100644
--- a/README.md
+++ b/README.md
@@ -16,28 +16,3 @@ To test, create `input` and `output` subfolders in the `data` directory. Create
 Re-Run: `docker-compose up --build`
 
 The testfile should be copied to the `data/output` directory.
-
-
-Read all input parameters from a config.json file. config.json is created by brainlife.io at runtime on the current working directory.
-Read all input data from paths specified in config.json (config.json contains both the input parameters; such as command line arguments as well as paths to data files; like t1.nii.gz)
-Write all output files in the current directory (./), in a structure defined as a Brainlife datatype. More information about Brainlife datatypes.
-
-App Development Timeline
-You would normally follow these steps to develop and register your App on Brainlife.
-
-Develop an algorithm that runs on your laptop or local cluster with your test datasets.
-Create a sample config.json file.
-Create main that parses config.json and passes it to your algorithm.
-Publish it as public github repo.
-Register your App on Brainlife. During this step, you can define what parameters and input file(s) should be made available to your App via config.json.
-Contact resource administrators and ask them to enable your App (more below).
-
-examples:
-https://github.com/BrainlifeMEEG/app-ICA-apply/tree/master
-Datatype: https://brainlife.io/app/63358285db978c7991a30e5b
-
-References:
-https://github.com/brainlife/abcd-spec
-https://brainlife.io/docs/apps/introduction/
-https://brainlife.io/docs/user/datatypes/
-https://brainlife.io/docs/apps/register/