From 9f5d29846b515283013e3ef180fc31e68163ffec Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 11 Aug 2023 15:35:44 +0200
Subject: [PATCH 1/3] Fix tool test inputs with multiple locations

---
 lib/galaxy/tools/test.py | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index 695f6c9ef7f..f440e5ff3cd 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -183,16 +183,25 @@ def _process_raw_inputs(
                 param_value = raw_input_dict["value"]
                 param_extra = raw_input_dict["attributes"]
                 location = param_extra.get("location")
-                if param_value is None and location:
-                    # If no value is given, we try to get the file name directly from the URL
-                    param_value = os.path.basename(location)
                 if not value.type == "text":
                     param_value = _split_if_str(param_value)
                 if isinstance(value, galaxy.tools.parameters.basic.DataToolParameter):
-                    if not isinstance(param_value, list):
-                        param_value = [param_value]
-                    for v in param_value:
-                        _add_uploaded_dataset(context.for_state(), v, param_extra, value, required_files)
+                    if param_value is None and location:
+                        # We get the input/s from the location which can be a list of urls separated by commas
+                        locations = _split_if_str(location)
+                        param_value = []
+                        for location in locations:
+                            v = os.path.basename(location)
+                            param_value.append(v)
+                            # param_extra should contain only the corresponding location
+                            extra = dict(param_extra)
+                            extra["location"] = location
+                            _add_uploaded_dataset(context.for_state(), v, extra, value, required_files)
+                    else:
+                        if not isinstance(param_value, list):
+                            param_value = [param_value]
+                        for v in param_value:
+                            _add_uploaded_dataset(context.for_state(), v, param_extra, value, required_files)
                     processed_value = param_value
                 elif isinstance(value, galaxy.tools.parameters.basic.DataCollectionToolParameter):
                     assert "collection" in param_extra

From 70c467b90ef3245bcf0a6b597e5600fc62bae925 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 18 Aug 2023 15:26:42 +0200
Subject: [PATCH 2/3] Fix location in collections

---
 lib/galaxy/tool_util/parser/xml.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 1b854c5b993..9b8b70ef687 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -864,6 +864,9 @@ def __parse_param_elem(param_elem, i=0):
     else:
         value = None
 
+    if value is None and attrib.get("location", None) is not None:
+        value = os.path.basename(attrib["location"])
+
     children_elem = param_elem
     if children_elem is not None:
         # At this time, we can assume having children only

From 9e193ef1e1b2ea6ba00f5282884c7a933223d609 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 18 Aug 2023 16:33:10 +0200
Subject: [PATCH 3/3] Consider multiple locations only with multiple=true

---
 lib/galaxy/tools/test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index f440e5ff3cd..ab3de3cf6ed 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -186,7 +186,7 @@ def _process_raw_inputs(
                 if not value.type == "text":
                     param_value = _split_if_str(param_value)
                 if isinstance(value, galaxy.tools.parameters.basic.DataToolParameter):
-                    if param_value is None and location:
+                    if location and value.multiple:
                         # We get the input/s from the location which can be a list of urls separated by commas
                         locations = _split_if_str(location)
                         param_value = []