--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/relate_objects.xml	Thu Mar 26 17:44:27 2020 -0400
@@ -0,0 +1,156 @@
+<tool id="cp_relate_objects" name="RelateObjects" version="@CP_VERSION@">
+    <description>assigns relationships parent-children between objects</description>
+    <macros>
+        <import>macros.xml</import>
+        <xml name="distToOtherParents">
+            <conditional name="con_other_parent_dist">
+                <param name="calc_dist_to_others" label="Calculate distances to other parents?" display="radio" type="select">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="Yes">
+                    <repeat name="rpt_parent_name" title="Parent Name">
+                        <param name="other_parent_name" type="text" label="Parent name">
+                            <expand macro="text_validator" />
+                        </param>
+                    </repeat>
+                </when>
+                <when value="No" />
+            </conditional>
+        </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 writero():
+    _str = "\nRelateObjects:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:5|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    _str += FOURSPACES + "Parent objects:%s\n" % params['parent_objects']
+
+    _str += FOURSPACES + "Child objects:%s\n" % params['child_objects']
+    _str += FOURSPACES + "Calculate child-parent distances?:%s\n" % params['con_dist']['calc_dist']
+    _str += FOURSPACES + "Calculate per-parent means for all child measurements?:%s\n" % params['means_for_all']
+
+    dist_others = params['con_dist']['con_other_parent_dist']['calc_dist_to_others']
+
+    _str += FOURSPACES + "Calculate distances to other parents?:%s\n" % dist_others
+
+    name_flag = params['con_save_child']['save_child_as_new']
+    _str += FOURSPACES + "Do you want to save the children with parents as a new object set?:%s\n" % name_flag
+
+    if name_flag == "Yes":
+        _str += FOURSPACES + "Name the output object:%s\n" % params['con_save_child']['name_output']
+    else:
+        _str += FOURSPACES + "Name the output object:None\n"
+
+    if dist_others == "Yes":
+        for pname in params['con_dist']['con_other_parent_dist']['rpt_parent_name']:
+            _str += FOURSPACES + "Parent name:%s\n" % pname['other_parent_name']
+
+    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(writero())
+
+f.close()
+        </configfile>
+    </configfiles>
+  
+    <inputs>
+        <expand macro="input_pipeline_macro"/>
+        <param name="parent_objects" label="Parent objects" type="text">
+            <expand macro="text_validator" />
+        </param>
+        <param name="child_objects" label="Child objects" type="text" >
+            <expand macro="text_validator" />
+        </param>
+        <param name="means_for_all" label="Calculate per-parent means for all child measurements?:" display="radio" type="select">      
+            <option value="Yes">Yes</option>
+            <option value="No">No</option>
+        </param>
+        <conditional name="con_dist">
+            <param name="calc_dist" label="Calculate child-parent distances?" type="select">
+                <option value="None">None</option>
+                <option value="Centroid">Centroid</option>
+                <option value="Minimum">Minimum</option>
+                <option value="Both">Both</option>
+            </param>
+            <when value="Centroid">
+                <expand macro="distToOtherParents" />
+            </when>
+            <when value="Minimum">
+                <expand macro="distToOtherParents" />
+            </when>
+            <when value="Both">
+                <expand macro="distToOtherParents" />
+            </when>
+            <when value="None" />
+        </conditional>
+        <conditional name="con_save_child">
+            <param name="save_child_as_new" label="Do you want to save the children with parents as a new object set?" display="radio" type="select">
+                <option value="Yes">Yes</option>
+                <option value="No">No</option>
+            </param>
+            <when value="Yes">
+                <param name="name_output" type="text" label="Name the output object">
+                    <expand macro="text_validator" />
+                </param>
+            </when>
+            <when value="No" />
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_macro" />
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param" />
+
+            <param name="parent_objects" value="Nuclei" />
+            <param name="child_objects" value="Nucleoli" />
+            <param name="means_for_all" value="Yes" />
+            <conditional name="con_dist">
+                <param name="calc_dist" value="Both" />
+                <conditional name="con_other_parent_dist">
+                    <param name="calc_dist_to_others" value="No" />
+                </conditional>
+            </conditional>
+            <conditional name="con_save_child">
+                <param name="save_child_as_new" value="Yes" />
+                <param name="name_output" value="RelateObjects" />
+            </conditional>
+
+            <expand macro="test_out_file" file="relate_objects.txt" />
+        </test>
+    </tests>
+
+    <expand macro="help" module="RelateObjects" />
+    <expand macro="citations" />
+
+</tool>