diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index e08f3fc194a..9cfbabd94f0 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -2110,7 +2110,6 @@ def _expand_multiple_inputs(kwargs, mode):
        _split_inputs(kwargs, mode)
 
     # Build up every combination of inputs to be run together.
-    #input_combos = [single_inputs]
     input_combos = _extend_with_matched_combos(single_inputs, matched_multi_inputs)
     input_combos = _extend_with_multiplied_combos(input_combos, multiplied_multi_inputs)
 
@@ -2172,17 +2171,18 @@ def _split_inputs(kwargs, mode):
     """
     input_keys = filter(lambda a: a.endswith('|input'), kwargs)
     single_inputs = {}
-    multi_inputs = {}
+    matched_multi_inputs = {}
+    multiplied_multi_inputs = {}
     for input_key in input_keys:
         input_val = kwargs[input_key]
         if isinstance(input_val, list):
-            multi_inputs[input_key] = input_val
+            input_base = input_key[:-len("|input")]
+            mode_key = "%s|multi_mode" % input_base
+            mode = kwargs.get(mode_key, "matched")
+            if mode == "matched":
+                matched_multi_inputs[input_key] = input_val
+            else:
+                multiplied_multi_inputs[input_key] = input_val
         else:
             single_inputs[input_key] = input_val
-    matched_multi_inputs = {}
-    multiplied_multi_inputs = {}
-    if mode == "product":
-        multiplied_multi_inputs = multi_inputs
-    else:
-        matched_multi_inputs = multi_inputs
     return (single_inputs, matched_multi_inputs, multiplied_multi_inputs)
diff --git a/static/images/silk/link.png b/static/images/silk/link.png
new file mode 100644
index 00000000000..25eacb7c252
Binary files /dev/null and b/static/images/silk/link.png differ
diff --git a/static/images/silk/link_break.png b/static/images/silk/link_break.png
new file mode 100644
index 00000000000..523575306d5
Binary files /dev/null and b/static/images/silk/link_break.png differ
diff --git a/templates/webapps/galaxy/workflow/run.mako b/templates/webapps/galaxy/workflow/run.mako
index 40852dc7527..72779d655c2 100644
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -33,12 +33,12 @@
                     } else {
                         select.val($('option:last', select).val());
                     }
+                    select.siblings('img').hide();
                     select.removeAttr('multiple').removeAttr('size');
                     placeholder = 'type to filter';
                 } else {
-                    // Comment out the following line to multiple batch input workflows in UI.
-                    $('.multiinput').addClass('disabled');
                     $('.multiinput', select.closest('.form-row')).removeClass('disabled');
+                    select.siblings('img').show();
                     select.attr('multiple', 'multiple').attr('size', 8);
                     placeholder = 'type to filter, [enter] to select all';
                 }
@@ -126,6 +126,57 @@
                 select.after(filter);
                 select.width(new_width);
             });
+
+            // Augment hidden fields with icons.
+            // http://stackoverflow.com/a/2088430
+            var imgOn='${h.url_for("/static/images/silk/link.png")}';
+            var imgOff='${h.url_for("/static/images/silk/link_break.png")}';
+            $(function(){
+                $(".multi-mode").each(function(){
+                    if($(this).val() == "matched") { 
+                        $(this).before($(document.createElement("img"))
+                            .attr({src:imgOn,title:'Checkbox', id:$(this).attr("id")})
+                            .css("display", $(this).css("display"))
+                            .addClass("chkBoxImg"));
+                    } else {
+                        $(this).before($(document.createElement("img"))
+                        .attr({src:imgOff, title:'Checkbox',id:$(this).attr("id")})
+                        .css("display", $(this).css("display"))
+                        .addClass("chkBoxImg"));
+                    }
+                });
+                $("img.chkBoxImg").click(function(){
+                    i= $(this).siblings("input[type=hidden]");
+                    s=$(this).attr("src");
+                    if(s==imgOn) {
+                        $(this).attr("src",imgOff);
+                        $(i).val("product");
+                    } else {
+                        $(this).attr("src",imgOn);
+                        $(i).val("matched");
+                    }
+                });
+            });
+            $("#tool_form").submit(function(e) {
+                var matchLength = -1;
+                $('span.multiinput_wrap select[name*="|input"]').each(function() {
+                    var value = $(this).val();
+                    if(value instanceof Array) {
+                        // Multi-value
+                        if($(this).siblings("input[type=hidden]").val() == "matched") {
+                            var length = $(this).val().length;
+                            if(matchLength == -1) {
+                                matchLength = length;
+                            } else if(length != matchLength) {
+                                e.preventDefault();
+                                alert("Linked inputs must be submitted in equal number.");
+                                return false;
+                            }
+                        }
+                    }
+                });
+                return true;
+            });
         });
     </script>
 </%def>
@@ -260,6 +311,7 @@ if wf_parms:
                     %if step.type == 'data_input':
                     ##Input Dataset Step, wrap for multiinput.
                         <span class='multiinput_wrap'>
+                        <input class="multi-mode" type="hidden" name="${str(step.id)}|multi_mode" id="${str(step.id)}|multi_mode" value="matched" />
                         ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
                         </span>
                     %else:
@@ -340,30 +392,6 @@ if wf_parms:
 <form id="tool_form" name="tool_form" method="POST">
 ## <input type="hidden" name="workflow_name" value="${h.to_unicode( workflow.name ) | h}" />
 
-<!-- TODO: Implement UI for selecting between product and matched mode
-     for batch workflows in multiple inputs are selected for 2 or more
-     params.
-
-     1) Delete this line above: $('.multiinput').addClass('disabled');
-     2) Allow user to select between product and matched mode.
-
-     If user selected 5 inputs for one param and 5 inputs for another
-     in matched mode that will be run the workflow 5 times matching
-     each input and in product mode it will run the workflow 25 times
-     with every combination of input pairs. If user selects 6 inputs
-     for one param and 4 for another, in product mode 24 workflows
-     will run and in matched mode the submission will fail.
-
-     In matched mode the inputs are matched from top to bottom
-     regardless of the order they are actually select in. This
-     behavior is I assume the desired behavior but I have only tested
-     it in chrome, care should be taken to test behavior on other
-     browsers and augment UI to ensure numbers of inputs matches
-     up.
--->
-<input type="hidden" name="multiple_input_mode" value="matched" /> <!-- product or matched -->
-
-
 %if wf_parms:
 <div class="metadataForm">
     <div class="metadataFormTitle">Workflow Parameters</div>