diff measure_texture.xml @ 3:658a2a451aec draft

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

--- a/measure_texture.xml	Thu Apr 16 05:30:53 2020 -0400
+++ b/measure_texture.xml	Mon May 11 07:45:48 2020 -0400
@@ -1,11 +1,12 @@
 <tool id="cp_measure_texture" name="MeasureTexture" version="@CP_VERSION@">
-    <description>quantify their roughness and smoothness of the textures</description>
-  
+    <description>quantify the roughness and smoothness of the textures</description>
+
     <macros>
         <import>macros.xml</import>
         <xml name="measureImgObj">
-            <repeat name="rpt_obj_to_measure" title="Add another object">
-                <param name="obj_to_measure" label="Select objects to measure" type="text" />       
+            <repeat name="rpt_obj_to_measure" title="new object" min="1">
+
+                <param name="obj_to_measure" label="Enter the names of the objects to measure" type="text" />
             </repeat>
         </xml>
     </macros>
@@ -66,25 +67,33 @@
     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(writemi())
 
-f.close()
-        </configfile>    
+    f.close()
+        </configfile>
     </configfiles>
-  
+
     <inputs>
+        <expand macro="input_pipeline_param" />
+        <repeat name="rpt_image_to_measure" title="new image" min="1">
 
-        <expand macro="input_pipeline_macro" />
-        <repeat name="rpt_image_to_measure" title="Add another image">
-            <param name="image_to_measure" label="Select an image to measure" type="text" >
+            <param name="image_to_measure" label="Enter the name of an image to measure" type="text">
                 <expand macro="text_validator" />
             </param>
         </repeat>
 
         <conditional name="con_img_obj">
             <param name="img_obj" label="Measure images or objects?" type="select">
+                <help>
+                    <![CDATA[
+                        This setting determines whether the module computes image-wide measurements, per-object measurements or both.
+                        <br> - Images: Select if you only want to measure the texture across entire images.
+                        <br> - Objects: Select if you want to measure the texture on a per-object basis only.
+                        <br> - Both: Select to make both image and object measurements.
+                        ]]>
+                </help>
                 <option value="Images">Images</option>
                 <option value="Objects">Objects</option>
                 <option value="Both">Both</option>
@@ -97,13 +106,18 @@
             </when>
             <when value="Images" />
         </conditional>
-        <repeat name="rpt_scale_to_measure" title="Add another scale">
-            <param name="scale_to_measure" label="Texture scale to measure" type="integer" value="3" min="0" />
+        <repeat name="rpt_scale_to_measure" title="new scale" min="1">
+            <param name="scale_to_measure" label="Texture scale to measure" type="integer" value="3" min="0">
+                <help>
+                    You can specify the scale of texture to be measured, in pixel units. The texture scale is the distance between correlated intensities in the image. A higher number for the scale of texture measures larger patterns of texture whereas smaller numbers measure more localized patterns of texture. It is best to measure texture on a scale smaller than your objects’ sizes, so be sure that the value entered for the scale of texture is smaller than most of your objects. For very small objects (smaller than the scale of texture you are measuring), the texture cannot be measured and will result in an undefined value in the output file.
+
+                </help>
+            </param>
         </repeat>
     </inputs>
 
     <outputs>
-        <expand macro="output_pipeline_macro" />
+        <expand macro="output_pipeline_param" />
     </outputs>
 
     <tests>
@@ -123,10 +137,26 @@
                 <param name="scale_to_measure" value="3" />
             </repeat>
 
-            <expand macro="test_out_file" file="measure_texture.txt" />
+            <expand macro="test_out_file" file="measure_texture.cppipe" />
         </test>
     </tests>
 
-    <expand macro="help" module="MeasureObjectSizeShape" />
-    <expand macro="citations" /> 
+    <help>
+        <![CDATA[
+
+            .. class:: infomark
+
+            **What it does**
+
+            MeasureTexture measures the degree and nature of textures within images and objects to quantify their roughness and smoothness.
+            This module measures intensity variations in grayscale images.
+            An object or entire image without much texture has a smooth appearance; an object or image with a lot of texture will appear rough and show a wide variety of pixel intensities.
+            Note that any input objects specified will have their texture measured against all input images specified, which may lead to image-object texture combinations that are unnecessary.
+            If you do not want this behavior, use multiple MeasureTexture modules to specify the particular image-object measures that you want.
+
+            @COMMON_HELP@
+            ]]>
+    </help>
+
+    <expand macro="citations" />
 </tool>