Mercurial > repos > bgruening > vpt_segment

diff macros.xml @ 2:a88a1e78702e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
author bgruening
date Sun, 22 Jun 2025 12:25:48 +0000
parents ed28a1feba82
children 0811613196a2
line wrap: on
line diff
--- a/macros.xml	Mon May 26 06:54:28 2025 +0000
+++ b/macros.xml	Sun Jun 22 12:25:48 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirements>
@@ -63,6 +63,68 @@
             <filter>advanced_output['log']</filter>
         </data>
     </xml>
+    <xml name="task_input_data">
+        <conditional name="normalize_conditional">
+            <param name="normalize_select" type="select" label="Perform Normalization?">
+                <option value="Yes" selected="true">Yes</option>
+                <option value="No">No</option>
+            </param>
+            <when value="Yes">
+                <conditional name="normalize_type_conditional" label="Select normalization method">
+                    <expand macro="normalization_param"/>
+                    <when value="default"/>
+                    <when value="CLAHE">
+                        <param name="clip_limit" type="float" min="0" max="1" value="0.01" label="Clip limit" help="higher values give more contrast"/>
+                        <param name="filter_size" type="integer" min="1" value="100" label="Tile grid size"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="No"/>
+        </conditional>
+        <conditional name="blur_conditional">
+            <param name="blur_select" type="select" label="Perform Blur?">
+                <option value="Yes">Yes</option>
+                <option value="No" selected="true">No</option>
+            </param>
+            <when value="Yes">
+                <param name="blur_options" type="select" label="Blur options">
+                    <option value="average">average</option>
+                    <option value="median">median</option>
+                    <option value="gaussian">gaussian</option>
+                </param>
+                <param name="kernel_size" type="integer" min="0" value="5" label="Kernel size in pixel"/>
+            </when>
+            <when value="No"/>
+        </conditional>
+        <conditional name="downsample_conditional">
+            <param name="downsample_select" type="select" label="Perform downsample?">
+                <option value="Yes">Yes</option>
+                <option value="No" selected="true">No</option>
+            </param>
+            <when value="Yes">
+                <param name="scale" type="float" min="0" value="2.0" label="Downsample" help="Reduces the size of the images during segmentation to decrease processing time" />
+            </when>
+            <when value="No"/>
+        </conditional>
+    </xml>
+    <xml name="channel_map_conditional_childs">
+        <when value="None"/>
+        <when value="DAPI">
+            <expand macro="task_input_data"/>
+        </when>
+        <when value="PolyT">
+            <expand macro="task_input_data"/>
+        </when>
+        <when value="Cellbound1">
+            <expand macro="task_input_data"/>
+        </when>
+        <when value="Cellbound2">
+            <expand macro="task_input_data"/>
+        </when>
+        <when value="Cellbound3">
+            <expand macro="task_input_data"/>
+        </when>
+    </xml>
     <xml name="sanitize_digits">
         <sanitizer invalid_char="">
             <valid initial="string.digits">