Change CSV to TSV

README.md

@@ -53,7 +53,7 @@ Galaxy Tool extractor
     $ python bin/extract_all_tools.sh
     ```
 
-The script will generate a CSV file with each tool found in the list of GitHub repositories and metadata for these tools:
+The script will generate a TSV file with each tool found in the list of GitHub repositories and metadata for these tools:
 
 1. Galaxy wrapper id
 2. Description

bin/extract_all_tools.sh

@@ -3,4 +3,4 @@
 python bin/extract_galaxy_tools.py \
         extractools \
         --api $GITHUB_API_KEY \
-        --all_tools 'results/all_tools.csv'
+        --all_tools 'results/all_tools.tsv'

bin/extract_galaxy_tools.py

@@ -388,16 +388,16 @@ def filter_tools(tools: List[Dict], ts_cat: List[str], excluded_tools: List[str]
     # Extract tools
     extractools = subparser.add_parser("extractools", help="Extract tools")
     extractools.add_argument("--api", "-a", required=True, help="GitHub access token")
-    extractools.add_argument("--all_tools", "-o", required=True, help="Filepath to CSV with all extracted tools")
+    extractools.add_argument("--all_tools", "-o", required=True, help="Filepath to TSV with all extracted tools")
     # Filter tools
     filtertools = subparser.add_parser("filtertools", help="Filter tools")
     filtertools.add_argument(
         "--tools",
         "-t",
         required=True,
-        help="Filepath to CSV with all extracted tools, generated by extractools command",
+        help="Filepath to TSV with all extracted tools, generated by extractools command",
     )
-    filtertools.add_argument("--filtered_tools", "-f", required=True, help="Filepath to CSV with filtered tools")
+    filtertools.add_argument("--filtered_tools", "-f", required=True, help="Filepath to TSV with filtered tools")
     filtertools.add_argument(
         "--categories", "-c", help="Path to a file with ToolShed category to keep in the extraction (one per line)"
     )

bin/filter_microgalaxy_tools.sh

@@ -14,8 +14,8 @@ mkdir -p 'results/microgalaxy'
 
 python bin/extract_galaxy_tools.py \
         filtertools \
-        --tools 'results/all_tools.csv' \
-        --filtered_tools 'results/microgalaxy/tools.csv' \
+        --tools 'results/all_tools.tsv' \
+        --filtered_tools 'results/microgalaxy/tools.tsv' \
         --categories "data/microgalaxy/categories" \
         --exclude "data/microgalaxy/tools_to_exclude" \
         --keep "data/microgalaxy/tools_to_keep"