--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gray_to_color.xml	Thu Mar 26 17:46:36 2020 -0400
@@ -0,0 +1,252 @@
+<tool id="cp_gray_to_color" name="GrayToColor" version="@CP_VERSION@">
+    <description>takes grayscale images and produces a color image from them</description>
+    <macros>
+        <import>macros.xml</import>
+        <xml name="rgb">
+            <param name="rgb_red" label="Select the image to be colored red" value="Leave this black" type="text"/>
+            <param name="rgb_red_weight" label="Relative weight for the red image" optional="true" type="float" value="0.8"/>
+
+            <param name="rgb_green" label="Select the image to be colored green" value="Leave this black" type="text"/>
+            <param name="rgb_green_weight" label="Relative weight for the green image" optional="true" type="float" value="1.0" />
+
+            <param name="rgb_blue" label="Select the image to be colored blue" value="Leave this black" type="text"/>
+            <param name="rgb_blue_weight" label="Relative weight for the blue image" optional="true" type="float" value="0.5"/>
+
+            <param name="name_output_image" label="Name the output image" value="ColorImage" type="text"/>      
+        </xml>
+        <xml name="cmyk">
+            <param name="cmyk_cyan" label="Select the image to be colored cyan" value="Leave this black" type="text"/>
+            <param name="cmyk_cyan_weight" label="Relative weight for the cyan image" optional="true" type="float" value="0.5"/>
+
+            <param name="cmyk_magenta" label="Select the image to be colored magenta" value="Leave this black" type="text"/>
+            <param name="rgb_green_weight" label="Relative weight for the green image" optional="true" type="float" value="0.0"/>
+
+            <param name="cmyk_yellow" label="Select the image to be colored yellow" value="Leave this black" type="text"/>
+            <param name="cmyk_yellow_weight" label="Relative weight for the yellow image" optional="true" type="float" value="0.0"/>
+
+            <param name="cmyk_brightness" label="Select the image that determines brightness" value="Leave this black" type="text"/>
+            <param name="cmyk_brightness_weight" label="Relative weight for the brightness image" optional="true" type="float" value="0.5"/>
+
+            <param name="name_output_image" label="Name the output image" value="ColorImage" type="text">
+                <expand macro="text_validator" />
+            </param>  
+          
+        </xml>
+        <xml name="stack">
+            <param name="name_output_image" label="Name the output image" value="ColorImage" type="text">
+                <expand macro="text_validator" />
+            </param>  
+            <repeat name="rpt_image_name" title="Add another channel">
+                <param name="image_name" type="text" label="Image name" >
+                    <expand macro="text_validator" />
+                </param>
+            </repeat>
+        </xml>
+        <xml name="composite">
+            <param name="name_output_image" label="Name the output image" value="ColorImage" type="text">
+                <expand macro="text_validator" />
+            </param>  
+            <repeat name="rpt_image_name" title="Add another channel">
+                <param name="image_name" type="text" label="Image name">
+                    <expand macro="text_validator" />
+                </param>
+                <param name="color" type="color" label="Color" />
+                <param name="weight" type="float" label="Weight" value="0.8" min="0.0" max="1.0" />
+            </repeat>      
+        </xml>
+    </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 writegtc():
+    _str = "\nGrayToColor:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\\'Combine masks nuclei + nucleoli with colors\\'\\x5D|batch_state:array(\\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    color_scheme = params['con_color_scheme']['color_scheme']
+
+    rgb_blue = params['con_color_scheme']['rgb_blue'] if 'rgb_blue' in params[
+        'con_color_scheme'] else 'Leave this black'
+    rgb_blue_weight = 1.0 if params['con_color_scheme']['rgb_blue_weight'] == "" else params['con_color_scheme'][
+        'rgb_blue_weight']
+
+    rgb_green = params['con_color_scheme']['rgb_green'] if 'rgb_green' in params[
+        'con_color_scheme'] else 'Leave this black'
+    rgb_green_weight = 1.0 if params['con_color_scheme']['rgb_green_weight'] == "" else params['con_color_scheme'][
+        'rgb_green_weight']
+
+    rgb_red = params['con_color_scheme']['rgb_red'] if 'rgb_red' in params['con_color_scheme'] else 'Leave this black'
+    rgb_red_weight = 1.0 if params['con_color_scheme']['rgb_red_weight'] == "" else params['con_color_scheme'][
+        'rgb_red_weight']
+
+    name_output_image = params['con_color_scheme']['name_output_image']
+
+    cmyk_cyan = params['con_color_scheme']['cmyk_cyan'] if 'cmyk_cyan' in params[
+        'con_color_scheme'] else 'Leave this black'
+
+    if 'cmyk_cyan_weight' in params['con_color_scheme']:
+        if params['con_color_scheme']['cmyk_cyan_weight'] == "":
+            cmyk_cyan_weight = 1.0
+        else:
+            cmyk_cyan_weight = params['con_color_scheme']['cmyk_cyan_weight']
+    else:
+        cmyk_cyan_weight = 1.0
+
+    cmyk_magenta = params['con_color_scheme']['cmyk_magenta'] if 'cmyk_magenta' in params[
+        'con_color_scheme'] else 'Leave this black'
+
+    if 'cmyk_magenta_weight' in params['con_color_scheme']:
+        if params['con_color_scheme']['cmyk_magenta_weight'] == "":
+            cmyk_magenta_weight = 1.0
+        else:
+            cmyk_magenta_weight = params['con_color_scheme']['cmyk_cyan_weight']
+    else:
+        cmyk_magenta_weight = 1.0
+
+    cmyk_yellow = params['con_color_scheme']['cmyk_yellow'] if 'cmyk_yellow' in params[
+        'con_color_scheme'] else 'Leave this black'
+
+    if 'cmyk_yellow_weight' in params['con_color_scheme']:
+        if params['con_color_scheme']['cmyk_yellow_weight'] == "":
+            cmyk_yellow_weight = 1.0
+        else:
+            cmyk_yellow_weight = params['con_color_scheme']['cmyk_yellow_weight']
+    else:
+        cmyk_yellow_weight = 1.0
+
+    cmyk_brightness = params['con_color_scheme']['cmyk_brightness'] if 'cmyk_brightness' in params[
+        'con_color_scheme'] else 'Leave this black'
+
+    if 'cmyk_brightness_weight' in params['con_color_scheme']:
+        if params['con_color_scheme']['cmyk_brightness_weight'] == "":
+            cmyk_brightness_weight = 1.0
+        else:
+            cmyk_brightness_weight = params['con_color_scheme']['cmyk_brightness_weight']
+    else:
+        cmyk_brightness_weight = 1.0
+
+    count = len(params['con_color_scheme']['rpt_image_name']) if 'rpt_image_name' in params['con_color_scheme'] else 1
+
+    _str += FOURSPACES + "Select a color scheme:%s\n" % color_scheme
+
+    _str += FOURSPACES + "Select the image to be colored red:%s\n" % rgb_red
+    _str += FOURSPACES + "Select the image to be colored green:%s\n" % rgb_green
+    _str += FOURSPACES + "Select the image to be colored blue:%s\n" % rgb_blue
+    _str += FOURSPACES + "Name the output image:%s\n" % name_output_image
+    _str += FOURSPACES + "Relative weight for the red image:%.1f\n" % rgb_red_weight
+    _str += FOURSPACES + "Relative weight for the green image:%.1f\n" % rgb_green_weight
+    _str += FOURSPACES + "Relative weight for the blue image:%.1f\n" % rgb_blue_weight
+
+    _str += FOURSPACES + "Select the image to be colored cyan:%s\n" % cmyk_cyan
+    _str += FOURSPACES + "Select the image to be colored magenta:%s\n" % cmyk_magenta
+    _str += FOURSPACES + "Select the image to be colored yellow:%s\n" % cmyk_yellow
+    _str += FOURSPACES + "Select the image that determines brightness:%s\n" % cmyk_brightness
+    _str += FOURSPACES + "Relative weight for the cyan image:%.1f\n" % cmyk_cyan_weight
+    _str += FOURSPACES + "Relative weight for the magenta image:%.1f\n" % cmyk_magenta_weight
+    _str += FOURSPACES + "Relative weight for the yellow image:%.1f\n" % cmyk_yellow_weight
+    _str += FOURSPACES + "Relative weight for the brightness image:%.1f\n" % cmyk_brightness_weight
+
+    _str += FOURSPACES + "Hidden:%d\n" % count
+
+    if 'rpt_image_name' in params['con_color_scheme']:
+        for i in params['con_color_scheme']['rpt_image_name']:
+            image_name = params['con_color_scheme']['rpt_image_name']['image_name']
+            if 'color' in params['con_color_scheme']['rpt_image_name']:
+                color = params['con_color_scheme']['rpt_image_name']['color']
+            else:
+                color = '#FF0000'
+
+            if 'weight' in params['con_color_scheme']['rpt_image_name']:
+                weight = params['con_color_scheme']['rpt_image_name']['weight']
+            else:
+                weight = 1.0
+    else:
+        image_name = 'None'
+        color = '#FF0000'
+        weight = 1.0
+
+    _str += FOURSPACES + "Image name:%s\n" % image_name
+    _str += FOURSPACES + "Color:%s\n" % color
+    _str += FOURSPACES + "Weight:%s\n" % weight
+
+    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(writegtc())
+
+f.close()
+        </configfile>    
+    </configfiles>
+
+    <inputs>
+        <expand macro="input_pipeline_macro" />
+        <conditional name="con_color_scheme">
+            <param name="color_scheme" label="Select a color scheme" type="select">
+                <option value="RGB">RGB</option>
+                <option value="CMYK">CMYK</option>
+                <option value="Stack">Stack</option>
+                <option value="Composite">Composite</option>
+            </param>
+            <when value="RGB">
+                <expand macro="rgb" />
+            </when>
+            <when value="CMYK">
+                <expand macro="cmyk" />
+            </when>
+            <when value="Stack">
+                <expand macro="stack" />
+            </when>
+            <when value="Composite">
+                <expand macro="composite" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_macro" />
+    </outputs>
+
+    <tests>
+      <test>
+        <expand macro="test_input_pipeline_param" />
+        <conditional name="con_color_scheme">
+            <param name="color_scheme" value="RGB" />
+            <param name="rgb_red" value="MaskNucleoli" />
+            <param name="rgb_red_weight" value="0.8" />
+            <param name="rgb_green" value="Leave this black" />
+            <param name="rgb_blue" value="MaskNuclei" />
+            <param name="rgb_blue_weight" value="0.5" />
+            <param name="name_output_image" value="CombinedMask" />
+        </conditional>
+        <expand macro="test_out_file" file="gray_to_color.txt" />
+      </test>
+    </tests>
+
+    <expand macro="help" module="GrayToColor" />
+    <expand macro="citations" />
+
+</tool>