Update input and output labels

Delphine-L · Nov 21, 2024 · 3f4a97f · 3f4a97f
1 parent cd5b76e
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Showing 3 changed files with 24 additions and 24 deletions.
diff --git a/workflows/proteomics/clinicalmp/clinicalmp-database-generation/README.md b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/README.md
@@ -10,7 +10,7 @@ A GTN has been developed for this workflow. [https://training.galaxyproject.org/
 
 ### Search Databases (FASTA) from [Zenodo](https://zenodo.org/records/14181725)
 - `HUMAN SwissProt Protein_Database.fasta`
-- `Species UniProt FASTA.fasta`
+- `Species UniProt Protein Database FASTA.fasta`
 - `Contaminants (cRAP) Protein Database.fasta`
 ### MSMS files download from [Zenodo](https://zenodo.org/records/14181725)
 - `PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.mgf`

diff --git a/...cs/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation-tests.yml b/...cs/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation-tests.yml
@@ -1,18 +1,18 @@
 - doc: Test outline for iwc-clinicalmp-database-generation
   job:
-    HUMAN-SwissProt-Protein-Database:
+    Human SwissProt Protein Database:
       class: File
       location: https://zenodo.org/records/14181725/files/HUMAN-SwissProt-Protein-Database.fasta?download=1
       filetype: fasta
-    Species_UniProt_FASTA:
+    Species UniProt Protein Database:
       class: File
       location: https://zenodo.org/records/14181725/files/Species_UniProt_FASTA.fasta?download=1
       filetype: fasta
-    Contaminants-cRAP-Protein-Database:
+    Contaminants cRAP Protein Database:
       class: File
       location: https://zenodo.org/records/14181725/files/Contaminants(cRAP)-Protein-Database.fasta?download=1
       filetype: fasta
-    Input-MGF-files:
+    Tandem Mass Spectrometry (MS/MS) datasets:
       class: Collection
       collection_type: list
       elements:
@@ -37,7 +37,7 @@
       asserts:
         - that: has_text
           text: ">sp|"
-    CSV database:
+    Metanovo Compact CSV database:
       asserts:
         - that: has_text
           text: "index	Accession"

diff --git a/...roteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation.ga b/...roteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation.ga
@@ -18,18 +18,18 @@
     },
     "steps": {
         "0": {
-            "annotation": "HUMAN-SwissProt-Protein-Database",
+            "annotation": "Human SwissProt Protein Database",
             "content_id": null,
             "errors": null,
             "id": 0,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "HUMAN-SwissProt-Protein-Database",
-                    "name": "HUMAN-SwissProt-Protein-Database"
+                    "description": "Human SwissProt Protein Database",
+                    "name": "Human SwissProt Protein Database"
                 }
             ],
-            "label": "HUMAN-SwissProt-Protein-Database",
+            "label": "Human SwissProt Protein Database",
             "name": "Input dataset",
             "outputs": [],
             "position": {
@@ -45,18 +45,18 @@
             "workflow_outputs": []
         },
         "1": {
-            "annotation": "Input-MGF-files",
+            "annotation": "Tandem Mass Spectrometry (MS/MS) datasets",
             "content_id": null,
             "errors": null,
             "id": 1,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "Input-MGF-files",
-                    "name": "Input-MGF-files"
+                    "description": "Tandem Mass Spectrometry (MS/MS) datasets",
+                    "name": "Tandem Mass Spectrometry (MS/MS) datasets"
                 }
             ],
-            "label": "Input-MGF-files",
+            "label": "Tandem Mass Spectrometry (MS/MS) datasets",
             "name": "Input dataset collection",
             "outputs": [],
             "position": {
@@ -72,18 +72,18 @@
             "workflow_outputs": []
         },
         "2": {
-            "annotation": "Species_UniProt_FASTA",
+            "annotation": "Species UniProt Protein Database",
             "content_id": null,
             "errors": null,
             "id": 2,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "Species_UniProt_FASTA",
-                    "name": "Species_UniProt_FASTA"
+                    "description": "Species UniProt Protein Database",
+                    "name": "Species UniProt Protein Database"
                 }
             ],
-            "label": "Species_UniProt_FASTA",
+            "label": "Species UniProt Protein Database",
             "name": "Input dataset",
             "outputs": [],
             "position": {
@@ -99,18 +99,18 @@
             "workflow_outputs": []
         },
         "3": {
-            "annotation": "Contaminants-cRAP-Protein-Database",
+            "annotation": "Contaminants cRAP Protein Database",
             "content_id": null,
             "errors": null,
             "id": 3,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "Contaminants-cRAP-Protein-Database",
-                    "name": "Contaminants-cRAP-Protein-Database"
+                    "description": "Contaminants cRAP Protein Database",
+                    "name": "Contaminants cRAP Protein Database"
                 }
             ],
-            "label": "Contaminants-cRAP-Protein-Database",
+            "label": "Contaminants cRAP Protein Database",
             "name": "Input dataset",
             "outputs": [],
             "position": {
@@ -233,7 +233,7 @@
             "post_job_actions": {
                 "RenameDatasetActionoutput_csv": {
                     "action_arguments": {
-                        "newname": "CSV database"
+                        "newname": "Metanovo Compact CSV database"
                     },
                     "action_type": "RenameDatasetAction",
                     "output_name": "output_csv"
@@ -265,7 +265,7 @@
                     "uuid": "02940034-f0fe-4151-acd0-c6982e77b717"
                 },
                 {
-                    "label": "CSV database",
+                    "label": "Metanovo Compact CSV database",
                     "output_name": "output_csv",
                     "uuid": "d7208cb6-a907-4a8b-b8b7-cf44c103d14a"
                 }