diff --git a/planemo/commands/cmd_conda_env.py b/planemo/commands/cmd_conda_env.py
index 466b47afd..c16dae007 100644
--- a/planemo/commands/cmd_conda_env.py
+++ b/planemo/commands/cmd_conda_env.py
@@ -46,7 +46,7 @@ def cli(ctx, path, **kwds):
     """
     conda_context = build_conda_context(ctx, use_planemo_shell_exec=False, **kwds)
     conda_targets = collect_conda_targets(
-        path, conda_context=conda_context
+        ctx, path, conda_context=conda_context
     )
     installed_conda_targets = conda_util.filter_installed_targets(
         conda_targets, conda_context=conda_context
diff --git a/planemo/commands/cmd_conda_install.py b/planemo/commands/cmd_conda_install.py
index 5a2b2a232..883b02510 100644
--- a/planemo/commands/cmd_conda_install.py
+++ b/planemo/commands/cmd_conda_install.py
@@ -11,11 +11,11 @@
 
 
 @click.command('conda_install')
-@options.optional_tools_arg()
+@options.optional_tools_arg(multiple=True)
 @options.conda_target_options()
 @options.conda_auto_init_option()
 @command_function
-def cli(ctx, path, **kwds):
+def cli(ctx, paths, **kwds):
     """Install conda packages for tool requirements."""
     conda_context = build_conda_context(ctx, **kwds)
     if not conda_context.is_conda_installed():
@@ -36,7 +36,7 @@ def cli(ctx, path, **kwds):
             raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
 
     return_codes = []
-    for conda_target in collect_conda_targets(path):
+    for conda_target in collect_conda_targets(ctx, paths):
         ctx.log("Install conda target %s" % conda_target)
         return_code = conda_util.install_conda_target(
             conda_target, conda_context=conda_context
diff --git a/planemo/conda.py b/planemo/conda.py
index d3015922f..940718be9 100644
--- a/planemo/conda.py
+++ b/planemo/conda.py
@@ -7,9 +7,9 @@
 import os
 
 from galaxy.tools.deps import conda_util
-from galaxy.tools.loader_directory import load_tool_sources_from_path
 
 from planemo.io import shell
+from planemo.tools import yield_tool_sources_on_paths
 
 
 def build_conda_context(ctx, **kwds):
@@ -29,13 +29,18 @@ def build_conda_context(ctx, **kwds):
                                    shell_exec=shell_exec)
 
 
-def collect_conda_targets(path, found_tool_callback=None, conda_context=None):
-    """Load CondaTarget objects from supplied artifact sources."""
-    conda_targets = []
-    for (tool_path, tool_source) in load_tool_sources_from_path(path):
+def collect_conda_targets(ctx, paths, found_tool_callback=None, conda_context=None):
+    """Load CondaTarget objects from supplied artifact sources.
+
+    If a tool contains more than one requirement, the requirements will each
+    appear once in the output.
+    """
+    conda_targets = set([])
+    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, paths):
         if found_tool_callback:
             found_tool_callback(tool_path)
-        conda_targets.extend(tool_source_conda_targets(tool_source))
+        for target in tool_source_conda_targets(tool_source):
+            conda_targets.add(target)
     return conda_targets