From 610f90cf5bb5cb06e83c5c281febcb31c989dc7b Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 8 Feb 2024 11:11:05 +0100
Subject: [PATCH 1/2] add option to pass extra args to docker run

---
 planemo/galaxy/config.py | 2 ++
 planemo/options.py       | 9 +++++++++
 2 files changed, 11 insertions(+)

diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
index 4ec468175..570f077eb 100644
--- a/planemo/galaxy/config.py
+++ b/planemo/galaxy/config.py
@@ -130,6 +130,7 @@
             <param id="docker_sudo_cmd">${docker_sudo_cmd}</param>
             <param id="docker_cmd">${docker_cmd}</param>
             <param id="docker_volumes">${docker_volumes}</param>
+            <param id="docker_run_extra_arguments"><![CDATA[${docker_run_extra_arguments}]]></param>
             ${docker_host_param}
         </destination>
         <destination id="upload_dest" runner="planemo_runner">
@@ -1363,6 +1364,7 @@ def _handle_job_config_file(
                 "docker_cmd": str(kwds.get("docker_cmd", docker_util.DEFAULT_DOCKER_COMMAND)),
                 "docker_host_param": docker_host_param,
                 "docker_volumes": docker_volumes_str,
+                "docker_run_extra_arguments": kwds.get("docker_run_extra_arguments", ""),
             }
         )
         write_file(job_config_file, conf_contents)
diff --git a/planemo/options.py b/planemo/options.py
index 03f5eb3c1..8a61578e1 100644
--- a/planemo/options.py
+++ b/planemo/options.py
@@ -955,6 +955,14 @@ def docker_host_option():
         default=docker_util.DEFAULT_HOST,
     )
 
+def docker_run_extra_arguments_option():
+    return planemo_option(
+        "--docker_run_extra_arguments",
+        help="Extra arguments to pass to docker run.",
+        use_global_config=True,
+        default="",
+    )
+
 
 def docker_config_options():
     return _compose(
@@ -962,6 +970,7 @@ def docker_config_options():
         docker_sudo_option(),
         docker_host_option(),
         docker_sudo_cmd_option(),
+        docker_run_extra_arguments_option(),
     )
 
 

From 08eaf62dcb22217146f0d387cd8a25a0f2703d61 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 8 Feb 2024 14:15:18 +0100
Subject: [PATCH 2/2] Apply suggestions from code review

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 planemo/options.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/planemo/options.py b/planemo/options.py
index 8a61578e1..c17069787 100644
--- a/planemo/options.py
+++ b/planemo/options.py
@@ -955,6 +955,7 @@ def docker_host_option():
         default=docker_util.DEFAULT_HOST,
     )
 
+
 def docker_run_extra_arguments_option():
     return planemo_option(
         "--docker_run_extra_arguments",