# HG changeset patch
# User imgteam
# Date 1710310554 0
# Node ID 8bccb36e055a68538c98c30fb9c98b94ce10709a
# Parent  7db4fc31dbeef971dafb78c11a3022493fee90e2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit cb3d628f4c91e996e10dcb35b1168332e692293a

diff -r 7db4fc31dbee -r 8bccb36e055a auto_threshold.py
--- a/auto_threshold.py	Mon Mar 11 17:12:33 2024 +0000
+++ b/auto_threshold.py	Wed Mar 13 06:15:54 2024 +0000
@@ -43,7 +43,7 @@
     parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method')
     parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold')
     parser.add_argument('threshold', type=float, default=0, help='Manual thresholding value')
-    parser.add_argument('invert_output', default=False, type=bool, help='Values below/above the threshold are labeled with 0/255 if False, and with 255/0 otherwise')
+    parser.add_argument('--invert_output', default=False, action='store_true', help='Values below/above the threshold are labeled with 0/255 by default, and with 255/0 if this argument is used')
     args = parser.parse_args()
 
     do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.threshold, args.invert_output)
diff -r 7db4fc31dbee -r 8bccb36e055a auto_threshold.xml
--- a/auto_threshold.xml	Mon Mar 11 17:12:33 2024 +0000
+++ b/auto_threshold.xml	Wed Mar 13 06:15:54 2024 +0000
@@ -2,7 +2,7 @@
     <description>with scikit-image</description>
     <macros>
         <token name="@TOOL_VERSION@">0.18.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
@@ -23,7 +23,7 @@
     '$th_method.method_id'
     '$th_method.block_size'
     '$th_method.threshold'
-    '$invert_output'
+    $invert_output
     ]]>
     </command>
     <inputs>
@@ -72,7 +72,7 @@
                 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
             </when>
         </conditional>
-        <param name="invert_output" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
+        <param name="invert_output" type="boolean" checked="false" truevalue="--invert_output" falsevalue="" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
     </inputs>
     <outputs>
        <data format="tiff" name="output" from_work_dir="out.tif" />
diff -r 7db4fc31dbee -r 8bccb36e055a test-data/out3.tif
Binary file test-data/out3.tif has changed