diff imagej2_skeletonize3d.xml @ 1:269923244cc8 draft

planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:38:34 -0400
parents 8b787f641b9c
children 99f75b64cdf3
line wrap: on
line diff
--- a/imagej2_skeletonize3d.xml	Tue Aug 04 13:21:32 2015 -0400
+++ b/imagej2_skeletonize3d.xml	Wed Aug 26 14:38:34 2015 -0400
@@ -1,36 +1,27 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<tool id="imagej2_skeletonize3d" name="Skeletonize images" version="1.0.0">
+<tool id="imagej2_skeletonize3d" name="Skeletonize images" version="@WRAPPER_VERSION@.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="fiji_20141125_requirements" />
+    <expand macro="fiji_requirements" />
     <command>
 <![CDATA[
     python $__tool_directory__/imagej2_skeletonize3d.py
     --input "$input"
     --input_datatype $input.ext
-    @max_heap_size_args@
+    --black_background $black_background
     --jython_script $__tool_directory__/jython_script.py
     --output "$output"
-    --output_datatype $output_datatype
+    --output_datatype $output.ext
 ]]>
     </command>
     <inputs>
         <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
-        <param name="output_datatype" type="select" label="Save as format">
-            <expand macro="image_datatypes" />
-        </param>
-        <expand macro="max_heap_size_type_conditional" />
+        <expand macro="black_background_param" />
     </inputs>
     <outputs>
-        <data name="output" format_source="input" label="${tool.name} on ${on_string}">
-            <actions>
-                <action type="format">
-                    <option type="from_param" name="output_datatype" />
-                 </action>
-           </actions>
-       </data>
+        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
         <test>
@@ -50,12 +41,7 @@
 
 .. class:: warningmark
 
-The underlying AnalyzeSkeleton Fiji plugin works on binary images, so other image types will
-automatically be converted to binary before they are analyzed.  This step is performed using the
-ImageJ2 **Make Binary** command with the following settings: **Iterations:** 1, **Count:** 1,
-**Black background:** No, **Pad edges when eroding:** No.  If these settings are not appropriate,
-first manually convert the image to binary using the **Convert to binary (black and white) with
-ImageJ2** tool, which allows you to change them.
+@requires_binary_input@
 
 **What it does**