--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mask_image.xml	Thu Mar 26 17:47:02 2020 -0400
@@ -0,0 +1,113 @@
+<tool id="cp_mask_image" name="MaskImage" version="@CP_VERSION@">
+    <description>hides certain portions of an image based on previously identified objects or a binary image</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="py_requirements"/>
+    <expand macro="cmd_modules" />
+
+    <configfiles>
+        <inputs name="inputs"/>
+        <configfile name="script_file">
+import json
+import sys
+import os
+
+FOURSPACES=@SPACES@
+
+input_json_path = sys.argv[1]
+input_pipeline= sys.argv[2]
+
+params = json.load(open(input_json_path, "r"))
+
+def writemi():
+    _str = "\nMaskImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\'Keep only nucleoli inside the nuclei\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    _str += FOURSPACES + "Select the input image:%s\n" % params['input_image']
+    _str += FOURSPACES + "Name the output image:%s\n" % params['name_output_image']
+
+    img_obj = params['con_img_obj']['img_obj']
+
+    _str += FOURSPACES + "Use objects or an image as a mask?:%s\n" % params['con_img_obj']['img_obj']
+
+    if img_obj == "Objects":
+        _str += FOURSPACES + "Select object for mask:%s\n" % params['con_img_obj']['select_obj']
+        _str += FOURSPACES + "Select image for mask:None\n"
+    else:
+        _str += FOURSPACES + "Select object for mask:None\n"
+        _str += FOURSPACES + "Select image for mask:%s\n" % params['con_img_obj']['select_img']
+
+    _str += FOURSPACES + "Invert the mask?:%s\n" % params['invert_mask']
+
+    return _str
+
+with open(input_pipeline) as fin:
+    lines = fin.readlines()
+
+    k, v = lines[4].strip().split(':')
+
+    module_count = int(v)
+    new_count = module_count + 1
+    lines[4] = k + ":%d\n" % new_count
+
+    with open("output", "w") as f:
+        f.writelines(lines)
+        f.write(writemi())
+
+f.close()
+        </configfile>    
+    </configfiles>
+
+    <inputs>
+
+        <expand macro="input_pipeline_macro" />
+        <param name="input_image" label="Select input image" type="text">
+            <expand macro="text_validator" />
+        </param>
+
+        <param name="name_output_image" type="text" label="Name the output image">
+            <expand macro="text_validator" />
+        </param>
+
+        <conditional name="con_img_obj">
+            <param name="img_obj" label="Use objects or an image as a mask?" type="select">
+                <option value="Objects">Objects</option>
+                <option value="Image">Image</option>
+            </param>
+           <when value="Objects">
+               <param name="select_obj" label="Select object for mask" type="text"/>
+           </when>
+           <when value="Image">
+               <param name="select_img" label="Select image for mask" type="text"/>
+           </when>
+        </conditional>
+        <param name="invert_mask" label="Invert the mask?" type="select" display="radio">
+            <option value="Yes">Yes</option>
+            <option value="No">No</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_macro" />
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param"/>
+            <param name="input_image" value="DNAdarkholes" />
+            <param name="name_output_image" value="MaskDNAdarkholes" />
+            <conditional name="con_img_obj">
+                <param name="img_obj" value="Objects" />
+                <param name="select_obj" value="Nuclei" />
+            </conditional>
+            <param name="invert_mask" value="No" />
+            <expand macro="test_out_file" file="mask_image.txt" />
+        </test>
+    </tests>
+
+    <expand macro="help" module="GrayToColor" />
+    <expand macro="citations" />
+
+</tool>