From 8044da8ad5295806eb474e5c1fab8522a64caa99 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 1 Jul 2024 19:13:40 +0200
Subject: [PATCH] check lint skip types only for tool linting

---
 planemo/commands/cmd_lint.py |  9 +++++++++
 planemo/lint.py              | 10 +---------
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/planemo/commands/cmd_lint.py b/planemo/commands/cmd_lint.py
index 85a3c77cc..736e6d78a 100644
--- a/planemo/commands/cmd_lint.py
+++ b/planemo/commands/cmd_lint.py
@@ -4,11 +4,14 @@
 
 from planemo import options
 from planemo.cli import command_function
+from planemo.io import error
 from planemo.tool_lint import (
     build_tool_lint_args,
     lint_tools_on_path,
 )
 
+from galaxy.tool_util.lint import Linter
+
 
 @click.command("lint")
 @options.optional_tools_arg(multiple=True, allow_uris=True)
@@ -46,6 +49,12 @@
 def cli(ctx, uris, **kwds):
     """Check for common errors and best practices."""
     lint_args = build_tool_lint_args(ctx, **kwds)
+
+    linters = Linter.list_linters()
+    invalid_skip_types = list(set(lint_args["skip_types"]) - set(linters))
+    if len(invalid_skip_types):
+        error(f"Unknown linter type(s) {invalid_skip_types} in list of linters to be skipped. Known linters {linters}")
+
     exit_code = lint_tools_on_path(ctx, uris, lint_args, recursive=kwds["recursive"])
 
     # TODO: rearchitect XUnit.
diff --git a/planemo/lint.py b/planemo/lint.py
index c14247e7a..618bb61ed 100644
--- a/planemo/lint.py
+++ b/planemo/lint.py
@@ -4,10 +4,7 @@
 from urllib.request import urlopen
 
 import requests
-from galaxy.tool_util.lint import (
-    LintContext,
-    Linter,
-)
+from galaxy.tool_util.lint import LintContext
 
 from planemo.io import error
 from planemo.shed import find_urls_for_xml
@@ -34,11 +31,6 @@ def build_lint_args(ctx, **kwds):
                     continue
                 skip_types.append(line)
 
-    linters = Linter.list_linters()
-    invalid_skip_types = list(set(skip_types) - set(linters))
-    if len(invalid_skip_types):
-        error(f"Unknown linter type(s) {invalid_skip_types} in list of linters to be skipped. Known linters {linters}")
-
     lint_args = dict(
         level=report_level,
         fail_level=fail_level,