diff imagej2_bunwarpj_convert_to_raw.xml @ 1:7f9840d3b7e7 draft

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

--- a/imagej2_bunwarpj_convert_to_raw.xml	Tue Sep 17 17:06:56 2019 -0400
+++ b/imagej2_bunwarpj_convert_to_raw.xml	Mon Sep 28 16:48:49 2020 +0000
@@ -1,37 +1,43 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <tool id="imagej2_bunwarpj_convert_to_raw" name="Convert elastic transformation to raw" version="@WRAPPER_VERSION@.0">
     <description>with bUnwarpJ</description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="fiji_requirements" />
-    <command>
-<![CDATA[
-    python $__tool_directory__/imagej2_bunwarpj_convert_to_raw.py
-    --target_image "$target_image"
-    --target_image_format $target_image.ext
-    --source_image "$source_image"
-    --source_image_format $source_image.ext
-    --elastic_transformation "$elastic_transformation"
-    --raw_transformation "$raw_transformation"
-]]>
-    </command>
+    <expand macro="fiji_requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+#set output_log = 'output_log.txt'
+#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' '$target_with_ext' &&
+bunwarpj -convert_to_raw
+'$target_with_ext'
+'$source_with_ext'
+'$elastic_transformation'
+'$raw_transformation'
+&>'$output_log';
+if [[ $? -ne 0 ]]; then
+    cat '$output_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"/>
     </inputs>
     <outputs>
         <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
-        <data name="raw_transformation" format="txt" label="${tool.name} on ${on_string}: Raw transformation" />
+        <data name="raw_transformation" format="txt"/>
     </outputs>
     <tests>
         <test>
-            <param name="target_image" value="dotblot.jpg" />
-            <param name="source_image" value="blobs.gif" />
-            <param name="elastic_transformation" value="source_elastic_transformation.txt" ftype="txt" />
-            <output name="raw_transformation" file="source_raw_transformation.txt" ftype="txt" />
+            <expand macro="test_target_source_images"/>
+            <param name="elastic_transformation" value="source_elastic_transformation.txt" ftype="txt"/>
+            <output name="raw_transformation" file="source_raw_transformation.txt" ftype="txt"/>
         </test>
     </tests>
     <help>
@@ -45,5 +51,5 @@
 ]]>
 
     </help>
-    <expand macro="bunwarpj_citations" />
+    <expand macro="bunwarpj_citations"/>
 </tool>