diff measure_image_intensity.xml @ 3:2681008d726f draft

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

--- a/measure_image_intensity.xml	Thu Apr 16 05:42:27 2020 -0400
+++ b/measure_image_intensity.xml	Mon May 11 07:52:05 2020 -0400
@@ -1,6 +1,6 @@
 <tool id="cp_measure_image_intensity" name="MeasureImageIntensity" version="@CP_VERSION@">
     <description>measure several intensity features across an entire image</description>
-  
+
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -46,28 +46,27 @@
     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(writemii())
 
-f.close()
-        </configfile>    
+    f.close()
+        </configfile>
     </configfiles>
 
     <inputs>
-
-        <expand macro="input_pipeline_macro" />
-        <repeat name="rpt_intensity" title="Add another image">
-            <param name="image_to_measure" label="Select image to measure" type="text" >
+        <expand macro="input_pipeline_param" />
+        <repeat name="rpt_intensity" title="new image" min="1">
+            <param name="image_to_measure" label="Enter the name of the image to measure" type="text">
                 <expand macro="text_validator" />
             </param>
             <conditional name="con_intensity">
-                <param name="only_from_objects" label="Measure the intensity only from areas enclosed by objects?" display="radio" type="select">
+                <param name="only_from_objects" label="Measure the intensity only from areas enclosed by objects?" type="select" help="Select 'Yes' to measure only those pixels within an object type you choose, identified by a prior tool. Note that this module will aggregate intensities across all objects in the image: to measure each object individually, see MeasureObjectIntensity instead. ">
                     <option value="Yes">Yes</option>
                     <option value="No">No</option>
                 </param>
                 <when value="Yes">
-                    <param name="input_objects" label="Select the input objects" type="text">
+                    <param name="input_objects" label="Enter the name of the objects that the intensity will be aggregated within" type="text" help="The intensity measurement will be restricted to the pixels within these objects. ">
                         <expand macro="text_validator" />
                     </param>
                 </when>
@@ -77,7 +76,7 @@
     </inputs>
 
     <outputs>
-        <expand macro="output_pipeline_macro" />
+        <expand macro="output_pipeline_param" />
     </outputs>
 
     <tests>
@@ -96,9 +95,25 @@
                     <param name="input_objects" value="Nuclei" />
                 </conditional>
             </repeat>
-            <expand macro="test_out_file" file="measure_image_intensity.txt" />
+            <expand macro="test_out_file" file="measure_image_intensity.cppipe" />
         </test>
     </tests>
-    <expand macro="help" module="MeasureImageIntensity" />
+
+    <help>
+        <![CDATA[
+
+            .. class:: infomark
+
+            **What it does**
+
+            MeasureImageIntensity measures several intensity features across an entire image (excluding masked pixels).
+            For example, this module will sum all pixel values to measure the total image intensity. You can choose to measure all pixels in the image or restrict the measurement to pixels within objects that were identified in a prior module. If the image has a mask, only unmasked pixels will be measured.
+            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>