diff relate_objects.xml @ 3:f3f45c42bc36 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"

--- a/relate_objects.xml	Thu Apr 16 05:43:08 2020 -0400
+++ b/relate_objects.xml	Mon May 11 07:53:35 2020 -0400
@@ -72,28 +72,44 @@
     module_count = int(v)
     new_count = module_count + 1
     lines[4] = k + ":%d\n" % new_count
-    with open("output", "w") as f:
+    with open("output.cppipe", "w") as f:
         f.writelines(lines)
         f.write(writero())
 
-f.close()
+    f.close()
         </configfile>
     </configfiles>
-  
+
     <inputs>
-        <expand macro="input_pipeline_macro"/>
-        <param name="parent_objects" label="Parent objects" type="text">
+        <expand macro="input_pipeline_param"/>
+        <param name="parent_objects" label="Parent objects" value="Do not use" type="text" help="Parent objects are defined as those objects which encompass the child object. For example, when relating speckles to the nuclei that contain them, the nuclei are the parents.">
             <expand macro="text_validator" />
         </param>
-        <param name="child_objects" label="Child objects" type="text" >
+        <param name="child_objects" label="Child objects" value="Do not use" type="text" help="Child objects are defined as those objects contained within the parent object. For example, when relating speckles to the nuclei that contains them, the speckles are the children.">
             <expand macro="text_validator" />
         </param>
-        <param name="means_for_all" label="Calculate per-parent means for all child measurements?:" display="radio" type="select">      
+        <param name="means_for_all" label="Calculate per-parent means for all child measurements?" display="radio" type="select">
+            <help>
+                <![CDATA[
+                    Select 'Yes' to calculate the per-parent mean values of every upstream measurement made with the children objects and store them as a measurement for the parent. This module must be placed after all the measure modules that make measurements of the children objects.
+
+                    ]]>
+            </help>
             <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">
+                <help>
+                    <![CDATA[
+                        Choose the method to calculate distances of each child to its parent.
+                        For example, these measurements can tell you whether nuclear speckles are located more closely to the center of the nucleus or to the nuclear periphery.
+                        <br> - None: Do not calculate any distances. This saves computation time.
+                        <br> - Minimum: The distance from the centroid of the child object to the closest perimeter point on the parent object.
+                        <br> - Centroid: The distance from the centroid of the child object to the centroid of the parent.
+                        <br> - Both: Calculate both the Minimum and Centroid distances.
+                        ]]>
+                </help>
                 <option value="None">None</option>
                 <option value="Centroid">Centroid</option>
                 <option value="Minimum">Minimum</option>
@@ -111,12 +127,12 @@
             <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">
+            <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" help="Select 'Yes' to save the children objects that do have parents as new object set. Objects with no parents will be discarded.">
                 <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">
+                <param name="name_output" type="text" value="RelateObjects" label="Enter a name for the output object">
                     <expand macro="text_validator" />
                 </param>
             </when>
@@ -125,7 +141,7 @@
     </inputs>
 
     <outputs>
-        <expand macro="output_pipeline_macro" />
+        <expand macro="output_pipeline_param" />
     </outputs>
 
     <tests>
@@ -146,11 +162,29 @@
                 <param name="name_output" value="RelateObjects" />
             </conditional>
 
-            <expand macro="test_out_file" file="relate_objects.txt" />
+            <expand macro="test_out_file" file="relate_objects.cppipe" />
         </test>
     </tests>
 
-    <expand macro="help" module="RelateObjects" />
+    <help>
+        <![CDATA[
+
+            .. class:: infomark
+
+            **What it does**
+
+            RelateObjects assigns relationships; all objects (e.g., speckles) within a parent object (e.g., nucleus) become its children.
+            This module allows you to associate child objects with parent objects.
+            This is useful for counting the number of children associated with each parent, and for calculating mean measurement values for all children that are associated with each parent.
+            An object will be considered a child even if the edge is the only partly touching a parent object.
+            If a child object is touching multiple parent objects, the object will be assigned to the parent with maximal overlap.
+            For an alternate approach to assigning parent/child relationships, consider using the MaskObjects module.
+            If you want to include child objects that lie outside but still near parent objects, you might want to expand the parent objects using ExpandOrShrink or IdentifySecondaryObjects.
+
+            @COMMON_HELP@
+            ]]>
+    </help>
+
     <expand macro="citations" />
 
 </tool>