Mercurial > repos > iuc > imagej2_skeletonize3d
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 |
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--- 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**
