Mercurial > repos > imgteam > imagej2_enhance_contrast

diff imagej2_enhance_contrast.xml @ 3:1f92b1da556b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:04:54 +0000
parents 056e74fbbf6c
children
line wrap: on
line diff
--- a/imagej2_enhance_contrast.xml	Sun Nov 05 14:25:00 2023 +0000
+++ b/imagej2_enhance_contrast.xml	Wed Sep 25 16:04:54 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="imagej2_enhance_contrast" name="Enhance contrast" version="@WRAPPER_VERSION@.2">
+<tool id="imagej2_enhance_contrast" name="Enhance contrast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
@@ -13,15 +13,13 @@
     <expand macro="fiji_requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #import os
-#set error_log = '$output_log.txt'
 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
-#set input_with_ext = '.'.join([input_sans_ext, $input.ext])
+#set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
 ln -s '$input.file_name' '$input_with_ext' &&
 #set output_filename = '.'.join(['output', $input.ext])
 touch '$output_filename' &&
 ImageJ --ij2 --headless --debug
 --jython '$__tool_directory__/imagej2_enhance_contrast_jython_script.py'
-'$error_log'
 '$input_with_ext'
 '$equalize_histogram_cond.equalize_histogram'
 #if $equalize_histogram_cond.equalize_histogram == 'no':
@@ -33,12 +31,7 @@
 #end if
 '$output_filename'
 '$input.ext'
-&>'$error_log';
-if [[ $? -ne 0 ]]; then
-    cat '$error_log' >&2;
-else
-    mv '$output_filename' '$output';
-fi
+&& mv '$output_filename' '$output';
 ]]></command>
     <inputs>
         <expand macro="param_input"/>
@@ -66,18 +59,18 @@
         <test>
             <param name="input" value="blobs.gif"/>
             <param name="equalize_histogram" value="yes"/>
-            <output name="output" file="blobs_equalize.gif" compare="sim_size"/>
+            <output name="output" file="blobs_equalize.gif" compare="image_diff"/>
         </test>
         <test>
             <param name="input" value="blobs.gif"/>
             <param name="saturated_pixels" value="6.2"/>
-            <output name="output" file="blobs_saturate.gif" compare="sim_size"/>
+            <output name="output" file="blobs_saturate.gif" compare="image_diff"/>
         </test>
         <test>
             <param name="input" value="blobs.gif"/>
             <param name="saturated_pixels" value="13.0"/>
             <param name="normalize" value="yes"/>
-            <output name="output" file="blobs_normalize.gif" compare="sim_size"/>
+            <output name="output" file="blobs_normalize.gif" compare="image_diff"/>
         </test>
     </tests>
     <help>