diff convert_objects_to_image.xml @ 3:a23af23c3134 draft

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

--- a/convert_objects_to_image.xml	Thu Apr 16 09:11:27 2020 +0000
+++ b/convert_objects_to_image.xml	Mon May 11 11:35:07 2020 +0000
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="py_requirements"/>
-    <expand macro="cmd_modules" /> 
+    <expand macro="cmd_modules" />
     <configfiles>
         <inputs name="inputs" />
         <configfile name="script_file">
@@ -45,7 +45,7 @@
     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(writecoti())
 
@@ -54,11 +54,11 @@
     </configfiles>
 
     <inputs>
-        <expand macro="input_pipeline_macro" />
-        <param name="input_object" type="text" label="Select the input objects" />
-        <param name="name_output_image" type="text" label="Name the output image">
+        <expand macro="input_pipeline_param" />
+        <param name="input_object" type="text" label="Enter the name of the input objects you want to convert to an image" />
+        <param name="name_output_image" type="text" label="Enter the name of the resulting image">
             <expand macro="text_validator" />
-        </param> 
+        </param>
 
         <conditional name="con_color_format">
             <param name="color_format" type="select" label="Select the color format">
@@ -72,7 +72,7 @@
             <when value="Grayscale" />
             <when value="unit16" />
             <when value="Color">
-                <param name="color_map" type="select" label="Select the colormap">
+                <param name="color_map" type="select" label="Select the colormap" help="The colormap affects how the objects are colored." >
                     <option value="Default">Default</option>
                     <option value="Accent">Accent</option>
                     <option value="Blues">Blues</option>
@@ -138,7 +138,7 @@
     </inputs>
 
     <outputs>
-        <expand macro="output_pipeline_macro" />
+        <expand macro="output_pipeline_param" />
     </outputs>
 
     <tests>
@@ -149,9 +149,32 @@
             <conditional name="con_color_format">
                 <param name="color_format" value="Binary (black &amp; white)" />
             </conditional>
-            <expand macro="test_out_file" file="convert_objects_to_image.txt" />
+            <expand macro="test_out_file" file="convert_objects_to_image.cppipe" />
         </test>
     </tests>
-    <expand macro="help" module="ConvertObjectsToImage" />
+
+    <help>
+        <![CDATA[
+            .. class:: infomark
+
+            **What it does**
+
+            This module allows you to take previously identified objects and convert them into an image according to a colormap you select, which can then be saved with the *SaveImages* module. 
+            
+            For the *colormap*, you have the following options: 
+            
+            - *Color*: Allows you to choose a colormap that will produce jumbled colors for your objects. 
+            
+            - *Binary (black & white)*: All object pixels will be assigned 1 and all background pixels will be assigned 0, creating a binary image. 
+            
+            - *Grayscale*: Assigns all background pixels to 0 and each object a different number from 1 to 255 (the maximum value that you can put in an 8-bit integer) and numbers all pixels in each object with the object’s number. This creates an image where objects in the top left corner of the image are very dark and where the colors progress to white toward the bottom right corner of the image.
+            
+            - *uint16*: Assigns all background pixels to 0 and each object a different number from 1 to 65535 (the maximum value that you can put in a 16-bit integer) and numbers all pixels in each object with the object’s number. This creates an image where objects in the top left corner of the image are very dark and where the colors progress to white toward the bottom right corner of the image (though this can usually only be seen in a scientific image viewer since standard image viewers only handle 8-bit images).
+            
+            You can choose Color with a Gray colormap to produce jumbled gray objects. 
+            
+            @COMMON_HELP@
+            ]]>
+    </help>
     <expand macro="citations" />
 </tool>