--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_bunwarpj_raw_transform.xml	Fri Jun 19 16:59:58 2015 -0400
@@ -0,0 +1,83 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="1.0.0">
+    <description>with bUnwarpJ</description>
+    <macros>
+        <import>imagej2_macros.xml</import>
+    </macros>
+    <expand macro="fiji_headless_requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/imagej2_bunwarpj_raw_transform.py
+    --target_image "$target_image"
+    --target_image_format $target_image.ext
+    --source_image "$source_image"
+    --source_image_format $source_image.ext
+    --raw_transformation $raw_transformation
+    --source_out "$source_out"
+    --source_out_datatype $source_out_datatype
+    --jython_script $__tool_directory__/jython_script.py
+    --max_heap_size_type $set_max_heap_size.max_heap_size_type
+    --max_heap_size $set_max_heap_size.max_heap_size
+]]>
+    </command>
+    <inputs>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
+        <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
+        <param format="txt" name="raw_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in raw format"/>
+        <param name="source_out_datatype" type="select" label="Save registered source image as format">
+            <expand macro="image_datatypes" />
+        </param>
+        <expand macro="max_heap_size_type_conditional" />
+    </inputs>
+    <outputs>
+        <data name="source_out" format="png" label="${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="raw_transformation" value="source_raw_trans.txt" />
+            <param name="source_out_datatype" value="png" />
+            <output name="source_out" file="registered_source1.png" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+<![CDATA[
+Applies a raw transformation to an image, producing another image which is deformed according
+to the transformation.  The transformation file must be in the same format as the files created
+with the **Convert elastic transformation to raw with bUnwarpJ** tool.
+
+]]>
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @InProceedings(Arganda-Carreras2006,
+                author =     "Ignacio Arganda-Carreras and
+                                    Carlos Oscar S{\'a}nchez Sorzano and
+                                    Roberto Marabini and
+                                    Jos{\'e} Mar\'{\i}a Carazo and
+                                    Carlos Ortiz-de-Solorzano and
+                                    Jan Kybic",
+                title =          "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",    
+                publisher =  "Springer Berlin / Heidelberg",    
+                booktitle =   "Computer Vision Approaches to Medical Image Analysis",
+                series =       "Lecture Notes in Computer Science",
+                year =          "2006",
+                volume =      "4241",
+                pages =       "85-95",
+                month =       "May",
+                city =            "Graz, Austria")
+        </citation>
+        <citation type="doi">10.1038/nmeth.2019</citation>
+    </citations>
+</tool>