diff imagej2_bunwarpj_compare_raw.xml @ 1:9349961e09ce draft

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

--- a/imagej2_bunwarpj_compare_raw.xml	Tue Sep 17 17:06:19 2019 -0400
+++ b/imagej2_bunwarpj_compare_raw.xml	Mon Sep 28 16:50:39 2020 +0000
@@ -1,45 +1,49 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" version="@WRAPPER_VERSION@.0">
     <description>by warping index with bUnwarpJ</description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="fiji_requirements" />
-    <command>
-<![CDATA[
-    python $__tool_directory__/imagej2_bunwarpj_compare_raw.py
-    --target_image "$target_image"
-    --target_image_format $target_image.ext
-    --source_image "$source_image"
-    --source_image_format $source_image.ext
-    --target_raw_transformation "$target_raw_transformation"
-    --source_raw_transformation "$source_raw_transformation"
-    --output "$output"
-]]>
-    </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' '$target_with_ext' &&
+bunwarpj -compare_raw
+'$target_with_ext'
+'$source_with_ext'
+'$target_raw_transformation'
+'$source_raw_transformation'
+&>'$output_log';
+if [[ $? -ne 0 ]]; then
+    cat '$output_log' >&2;
+else
+    grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
+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"/>
         <param format="txt" name="target_raw_transformation" type="data" label="Raw transformation file 1"/>
         <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file 2"/>
     </inputs>
     <outputs>
-        <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}: Warping index" />
+        <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}"/>
     </outputs>
     <tests>
         <test>
-            <param name="target_image" value="dotblot.jpg" />
-            <param name="source_image" value="blobs.gif" />
-            <param name="target_raw_transformation" value="target_raw_transformation.txt" />
-            <param name="source_raw_transformation" value="source_raw_transformation.txt" />
-            <output name="output" file="warping_index1.txt" compare="contains" />
+            <expand macro="test_bunwarpj_raw_transform"/>
+            <output name="output" file="warping_index1.txt" compare="contains"/>
         </test>
         <test>
-            <param name="target_image" value="dotblot.jpg" />
-            <param name="source_image" value="blobs.gif" />
-            <param name="target_raw_transformation" value="source_raw_transformation.txt" />
-            <param name="source_raw_transformation" value="source_raw_transformation.txt" />
-            <output name="output" file="warping_index2.txt" />
+            <expand macro="test_target_source_images"/>
+            <param name="target_raw_transformation" value="source_raw_transformation.txt"/>
+            <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
+            <output name="output" file="warping_index2.txt"/>
         </test>
     </tests>
     <help>
@@ -53,5 +57,5 @@
 ]]>
 
     </help>
-    <expand macro="bunwarpj_citations" />
+    <expand macro="bunwarpj_citations"/>
 </tool>