From 88fb4507df60e1ae12d73580c1d8393c1aaae0eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Fri, 24 May 2024 15:36:48 +0200
Subject: [PATCH] Snake case argument names

---
 bin/extract_all_tools.sh      | 2 +-
 bin/extract_all_tools_test.sh | 4 ++--
 bin/extract_galaxy_tools.py   | 2 +-
 bin/get_community_tools.sh    | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/bin/extract_all_tools.sh b/bin/extract_all_tools.sh
index f4e03534..1926fac2 100755
--- a/bin/extract_all_tools.sh
+++ b/bin/extract_all_tools.sh
@@ -5,7 +5,7 @@ mkdir -p 'results/'
 python bin/extract_galaxy_tools.py \
         extractools \
         --api $GITHUB_API_KEY \
-        --all_tools 'results/all_tools.tsv'
+        --all-tools 'results/all_tools.tsv'
 
 python bin/create_interactive_table.py \
         --table "results/all_tools.tsv" \
diff --git a/bin/extract_all_tools_test.sh b/bin/extract_all_tools_test.sh
index 9960b9ea..22c4ac05 100755
--- a/bin/extract_all_tools_test.sh
+++ b/bin/extract_all_tools_test.sh
@@ -7,7 +7,7 @@ output="results/${1}_tools.tsv"
 python bin/extract_galaxy_tools.py \
         extractools \
         --api $GITHUB_API_KEY \
-        --all_tools $output \
-        --planemorepository $1 \
+        --all-tools $output \
+        --planemo-repository-list $1 \
         --test
 
diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py
index dae4009a..1eb7fc16 100644
--- a/bin/extract_galaxy_tools.py
+++ b/bin/extract_galaxy_tools.py
@@ -647,7 +647,7 @@ def filter_tools(
         help="Filepath to TSV with all extracted tools, generated by extractools command",
     )
     filtertools.add_argument(
-        "--filtered_tools",
+        "--filtered-tools",
         "-f",
         required=True,
         help="Filepath to TSV with filtered tools",
diff --git a/bin/get_community_tools.sh b/bin/get_community_tools.sh
index b3a6db3a..c0a2c610 100755
--- a/bin/get_community_tools.sh
+++ b/bin/get_community_tools.sh
@@ -12,7 +12,7 @@ for com_data_fp in data/communities/* ; do
                 python bin/extract_galaxy_tools.py \
                         filtertools \
                         --tools "results/all_tools.tsv" \
-                        --filtered_tools "results/$community/tools.tsv" \
+                        --filtered-tools "results/$community/tools.tsv" \
                         --categories "data/communities/$community/categories" \
                         --exclude "data/communities/$community/tools_to_exclude" \
                         --keep "data/communities/$community/tools_to_keep"