# HG changeset patch
# User bgruening
# Date 1745337015 0
# Node ID 6b341a048c2eea8a406be2874bc134ff108f6ef8
# Parent  8948cc562b7cf7729e9566b4836274b2dbae73a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6303638b71a30e15a36550af938ee35e49be560b

diff -r 8948cc562b7c -r 6b341a048c2e measureWoundClosing.groovy
--- a/measureWoundClosing.groovy	Thu Feb 29 17:43:50 2024 +0000
+++ b/measureWoundClosing.groovy	Tue Apr 22 15:50:15 2025 +0000
@@ -181,7 +181,7 @@
     rt.save(new File(outputDir, datasetId + ".csv").toString());
     // save binned image with ROI
     binnedImp.setRoi(scratchROI, false)
-    IJ.save(binnedImp, new File(outputDir, datasetId + ".tif").toString());
+    IJ.save(binnedImp, new File(outputDir, datasetId + ".tiff").toString());
 }
 
 println("Analysis of "+datasetId+" is done!")
diff -r 8948cc562b7c -r 6b341a048c2e woundhealing.xml
--- a/woundhealing.xml	Thu Feb 29 17:43:50 2024 +0000
+++ b/woundhealing.xml	Tue Apr 22 15:50:15 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="woundhealing_scratch_assay" name="Wound healing scratch assay" version="@VERSION@+galaxy0" profile="23.1">
+<tool id="woundhealing_scratch_assay" name="Wound healing scratch assay" version="@VERSION@+galaxy1" profile="23.1">
     <description>image analysis</description>
     <macros>
         <import>macros.xml</import>
@@ -15,7 +15,7 @@
             ln -s '$filename' './input/${filename.element_identifier}' &&
         #end for
     #end if
-    ImageJ --ij2 --headless 
+    ImageJ --ij2 --headless
     --run '$__tool_directory__/measureWoundClosing.groovy'
     'inputDir="./input",datasetId="$dataset_id",threshold="$threshold",headless="true",saveResults="true",outDirName="./output"'
     ]]>
@@ -25,7 +25,7 @@
             <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
                 <option value="yes">Yes</option>
                 <option value="no">No</option>
-            </param> 
+            </param>
             <when value="no">
                 <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
             </when>
@@ -37,7 +37,7 @@
         <param name="threshold"  type="text" label="CoV threshold (-1: auto)" value="-1"/>
     </inputs>
     <outputs>
-        <data name="tif_output" format="tif" from_work_dir="output/*.tif" label="movie output ${on_string}" />
+        <data name="tiff_output" format="tiff" from_work_dir="output/*.tiff" label="movie output ${on_string}" />
 	<data name="csv_output" format="tabular" from_work_dir="output/*.csv" label="tabular output"/>
     </outputs>
     <tests>
@@ -47,7 +47,7 @@
                 <param name="input_images" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/input/A3ROI2_Slow_0000.tif,https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/input/A3ROI2_Slow_0002.tif" />
 	    </conditional>
 	    <param name="dataset_id" value="A3ROI2_Slow" />
-	    <output name="tif_output" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/A3ROI2_Slow.tif"/>
+	    <output name="tiff_output" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/A3ROI2_Slow.tif"/>
 	    <output name="csv_output" file="A3ROI2_Slow.csv"/>
         </test>
     </tests>