diff imagej2_bunwarpj_elastic_transform.xml @ 1:39b2bc251b2f draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"

--- a/imagej2_bunwarpj_elastic_transform.xml	Tue Sep 17 17:10:48 2019 -0400
+++ b/imagej2_bunwarpj_elastic_transform.xml	Mon Sep 28 17:00:25 2020 +0000
@@ -1,48 +1,55 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.0">
+<tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.1">
     <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 $__tool_directory__/imagej2_bunwarpj_elastic_transform_jython_script.py
-]]>
-    </command>
+    <expand macro="fiji_requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+#set error_log = 'output_log.txt'
+touch '$error_log' &&
+
+## ImageJ2 requires file extensions to be valid image data types.
+#set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
+#set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
+ln -s '$source_image.file_name' '$source_with_ext' &&
+#set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
+#set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
+ln -s '$target_image.file_name' '$target_with_ext' &&
+
+bunwarpj -elastic_transform
+'$target_with_ext'
+'$source_with_ext'
+'$elastic_transformation'
+'$source_out'
+&>'$error_log';
+if [[ $? -ne 0 ]]; then
+    cat '$error_log' >&2;
+fi
+]]></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"/>
+        <expand macro="param_target_image"/>
+        <expand macro="param_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" />
+            <expand macro="image_datatypes"/>
         </param>
     </inputs>
     <outputs>
-        <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image">
+        <data name="source_out" format="png">
             <actions>
                 <action type="format">
-                    <option type="from_param" name="source_out_datatype" />
+                    <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" />
+            <expand macro="test_target_source_images"/>
+            <param name="elastic_transformation" value="blobs_direct_transf.txt"/>
+            <output name="source_out" file="elastic_trans_registered_source1.png" compare="sim_size"/>
         </test>
     </tests>
     <help>
@@ -57,5 +64,5 @@
 ]]>
 
     </help>
-    <expand macro="bunwarpj_citations" />
+    <expand macro="bunwarpj_citations"/>
 </tool>