diff imagej2_bunwarpj_elastic_transform.xml @ 0:301f24849032 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_bunwarpj_elastic_transform.xml	Tue Sep 17 17:10:48 2019 -0400
@@ -0,0 +1,61 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.0">
+    <description>with bUnwarpJ</description>
+    <macros>
+        <import>imagej2_macros.xml</import>
+    </macros>
+    <expand macro="fiji_requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/imagej2_bunwarpj_elastic_transform.py
+    --target_image "$target_image"
+    --target_image_format $target_image.ext
+    --source_image "$source_image"
+    --source_image_format $source_image.ext
+    --elastic_transformation $elastic_transformation
+    --source_out "$source_out"
+    --source_out_datatype $source_out_datatype
+    --jython_script $__tool_directory__/imagej2_bunwarpj_elastic_transform_jython_script.py
+]]>
+    </command>
+    <inputs>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
+        <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy -->
+        <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/>
+        <param name="source_out_datatype" type="select" label="Save registered source image as format">
+            <expand macro="image_datatypes" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image">
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="source_out_datatype" />
+                </action>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="target_image" value="dotblot.jpg" />
+            <param name="source_image" value="blobs.gif" />
+            <param name="elastic_transformation" value="blobs_direct_transf.txt" />
+            <param name="source_out_datatype" value="png" />
+            <output name="source_out" file="elastic_trans_registered_source1.png" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+<![CDATA[
+Applies an elastic transformation to an image, producing another image which is elastically
+deformed according to the transformation.  The transformation file must be in the same format
+as the files created with the **Save Transformation** option in the **Align two images with bUnwarpJ**
+tool.
+
+]]>
+
+    </help>
+    <expand macro="bunwarpj_citations" />
+</tool>