diff measure_object_intensity.xml @ 3:b867e9317a06 draft

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

--- a/measure_object_intensity.xml	Thu Apr 16 05:37:20 2020 -0400
+++ b/measure_object_intensity.xml	Mon May 11 07:49:31 2020 -0400
@@ -1,7 +1,9 @@
 <tool id="cp_measure_object_intensity" name="MeasureObjectIntensity" version="@CP_VERSION@">
     <description>measure several intensity features for identified objects</description>
 
-    <macros><import>macros.xml</import></macros>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
 
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
@@ -44,31 +46,31 @@
     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(writemoi())
 
-f.close()
-        </configfile>    
+    f.close()
+        </configfile>
     </configfiles>
 
     <inputs>
-        <expand macro="input_pipeline_macro" />
-        <repeat name="rpt_image" title="Add another image">
-            <param name="image_to_measure" label="Select an image to measure" type="text">
-              <expand macro="text_validator" />
+        <expand macro="input_pipeline_param" />
+        <repeat name="rpt_image" title="new image" min="1">
+            <param name="image_to_measure" label="Enter the name of an image to measure" type="text">
+                <expand macro="text_validator" />
             </param>
         </repeat>
 
-        <repeat name="rpt_object" title="Add another object">
-            <param name="objects_to_measure" label="Select objects to measure" type="text" >
-              <expand macro="text_validator" />
+        <repeat name="rpt_object" title="new object" min="1">
+            <param name="objects_to_measure" label="Enter the name of the objects to measure" type="text">
+                <expand macro="text_validator" />
             </param>
         </repeat>
     </inputs>
 
     <outputs>
-        <expand macro="output_pipeline_macro" />
+        <expand macro="output_pipeline_param" />
     </outputs>
 
     <tests>
@@ -77,14 +79,37 @@
             <repeat name="rpt_image">
                 <param name="image_to_measure" value="DNA"/>
             </repeat>
-            <repeat name="rpt_object" >
+            <repeat name="rpt_object">
                 <param name="objects_to_measure" value="Nuclei" />
             </repeat>
-            <expand macro="test_out_file" file="measure_object_intensity.txt" />
+            <expand macro="test_out_file" file="measure_object_intensity.cppipe" />
         </test>
     </tests>
-    
-    <expand macro="help" module="MeasureObjectIntensity" />
-    <expand macro="citations" /> 
+
+    <help>
+        <![CDATA[
+
+            .. class:: infomark
+
+            **What it does**
+
+            MeasureObjectIntensity measures several intensity features for identified objects.
+
+            Given an image with objects identified (e.g., nuclei or cells), this module extracts intensity features for each object based on one or more corresponding grayscale images.
+            Measurements are recorded for each object.
+            Intensity measurements are made for all combinations of the images and objects entered.
+            If you want only specific image/object measurements, you can use multiple MeasureObjectIntensity modules for each group of measurements desired.
+            Note that for publication purposes, the units of intensity from microscopy images are usually described as “Intensity units” or “Arbitrary intensity units” because microscopes are not calibrated to an absolute scale.
+            Also, it is important to note whether you are reporting the mean vs. the integrated intensity, so specify “Mean intensity units” or “Integrated intensity units” accordingly.
+            Keep in mind that the default behavior in CellProfiler is to rescale the image intensity from 0 to 1 by dividing all pixels in the image by the maximum possible intensity value.
+            This “maximum possible” value is defined by the “Set intensity range from” setting in NamesAndTypes; see the help for that setting for more details.
+
+            @COMMON_HELP@
+            ]]>
+    </help>
+
+
+
+    <expand macro="citations" />
 
 </tool>