From 9eaba5b565fde088613c09da01bc27853e9df950 Mon Sep 17 00:00:00 2001
From: Jalil Nourisa <jalil.nourisa@gmail.com>
Date: Mon, 4 Nov 2024 21:13:56 +0100
Subject: [PATCH] samll bug in renaming fixed

---
 src/api/comp_metric.yaml                                  | 5 +----
 ...e_perturbation_h5ad.yaml => file_evaluation_h5ad.yaml} | 0
 src/metrics/regression_1/config.vsh.yaml                  | 8 ++------
 .../batch_correction_evaluation/config.vsh.yaml           | 2 +-
 .../perturbation/batch_correction_seurat/config.vsh.yaml  | 2 +-
 src/workflows/process_perturbation/config.vsh.yaml        | 3 +--
 6 files changed, 6 insertions(+), 14 deletions(-)
 rename src/api/{file_perturbation_h5ad.yaml => file_evaluation_h5ad.yaml} (100%)

diff --git a/src/api/comp_metric.yaml b/src/api/comp_metric.yaml
index 26e1b1bbd..002569e30 100644
--- a/src/api/comp_metric.yaml
+++ b/src/api/comp_metric.yaml
@@ -69,15 +69,12 @@ functionality:
     - name: --skeleton 
       type: file
       direction: input
-      example: resources/prior/skeleton.csv'
+      example: resources/prior/skeleton.csv
     - name: --apply_skeleton 
       type: boolean
       direction: input
       default: true
 
-
-
-      
   test_resources:
     - type: python_script
       path: /src/common/component_tests/run_and_check_output.py
diff --git a/src/api/file_perturbation_h5ad.yaml b/src/api/file_evaluation_h5ad.yaml
similarity index 100%
rename from src/api/file_perturbation_h5ad.yaml
rename to src/api/file_evaluation_h5ad.yaml
diff --git a/src/metrics/regression_1/config.vsh.yaml b/src/metrics/regression_1/config.vsh.yaml
index ac984dd0d..a2c8c937a 100644
--- a/src/metrics/regression_1/config.vsh.yaml
+++ b/src/metrics/regression_1/config.vsh.yaml
@@ -1,4 +1,5 @@
 __merge__: ../../api/comp_metric.yaml
+
 functionality:
   name: regression_1
   namespace: "metrics"
@@ -7,13 +8,8 @@ functionality:
     summary: Calculates R2 score for regression 1
     description: |
       Calculates R2 score using regression approach 1.
+
   arguments:
-    - name: --min_tf
-      type: boolean
-      direction: input
-      description: calculate the scores for the given min tfs in addition to the default 
-      required: false
-      default: false
     - name: --binarize
       type: boolean 
       direction: input 
diff --git a/src/process_data/perturbation/batch_correction_evaluation/config.vsh.yaml b/src/process_data/perturbation/batch_correction_evaluation/config.vsh.yaml
index 41d7a7a92..9794ee946 100644
--- a/src/process_data/perturbation/batch_correction_evaluation/config.vsh.yaml
+++ b/src/process_data/perturbation/batch_correction_evaluation/config.vsh.yaml
@@ -7,7 +7,7 @@ functionality:
   
   arguments:
     - name: --perturbation_data
-      __merge__: ../../../api/file_perturbation_h5ad.yaml
+      __merge__: ../../../api/file_evaluation_h5ad.yaml
       required: true
       direction: input
     - name: --output
diff --git a/src/process_data/perturbation/batch_correction_seurat/config.vsh.yaml b/src/process_data/perturbation/batch_correction_seurat/config.vsh.yaml
index 6bc6a7752..15f1d87da 100644
--- a/src/process_data/perturbation/batch_correction_seurat/config.vsh.yaml
+++ b/src/process_data/perturbation/batch_correction_seurat/config.vsh.yaml
@@ -32,7 +32,7 @@ functionality:
       direction: input
       example: resources_test/grn-benchmark/perturbation_data.h5ad 
     - name: --perturbation_data_bc
-      __merge__: ../../../api/file_perturbation_h5ad.yaml
+      __merge__: ../../../api/file_evaluation_h5ad.yaml
       required: false
       direction: output
 
diff --git a/src/workflows/process_perturbation/config.vsh.yaml b/src/workflows/process_perturbation/config.vsh.yaml
index b61b72668..370169604 100644
--- a/src/workflows/process_perturbation/config.vsh.yaml
+++ b/src/workflows/process_perturbation/config.vsh.yaml
@@ -1,4 +1,3 @@
-
 __merge__: ../../api/unit_test.yaml
 
 functionality:
@@ -17,7 +16,7 @@ functionality:
       description: single cell perturbation data 
 
     - name: --perturbation_data_bc
-      __merge__: ../../api/file_perturbation_h5ad.yaml
+      __merge__: ../../api/file_evaluation_h5ad.yaml
       required: false
       direction: output