diff imagej2_analyze_skeleton.xml @ 2:9631aab7da53 draft

planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:36:10 -0400
parents dd8e4e000d2f
children 20555566d6ad
line wrap: on
line diff
--- a/imagej2_analyze_skeleton.xml	Tue Aug 04 13:19:34 2015 -0400
+++ b/imagej2_analyze_skeleton.xml	Wed Aug 26 14:36:10 2015 -0400
@@ -1,26 +1,27 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="1.0.0">
+<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="fiji_20141125_requirements" />
+    <expand macro="fiji_requirements" />
     <command>
 <![CDATA[
     python $__tool_directory__/imagej2_analyze_skeleton.py
     --input "$input"
     --input_datatype $input.ext
+    --black_background $black_background
     --prune_cycle_method $prune_cycle_method
     --prune_ends $prune_ends
     --calculate_largest_shortest_path $calculate_largest_shortest_path
-    --show_detailed_info $show_detailed_info
-    @max_heap_size_args@
+    ##TODO: seel below--show_detailed_info $show_detailed_info
     --jython_script $__tool_directory__/jython_script.py
     --output "$output"
 ]]>
     </command>
     <inputs>
         <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
+        <expand macro="black_background_param" />
         <param name="prune_cycle_method" type="select" label="Prune cycle method">
             <option value="none" selected="True">None</option>
             <option value="shortest_branch">Shortest branch</option>
@@ -35,11 +36,13 @@
             <option value="no" selected="True">No</option>
             <option value="yes">Yes</option>
         </param>
+        <!-- TODO: Uncomment this option when the tool has been enhanced to use the
+        future "Display labeled skeletons" option.  See http://fiji.sc/AnalyzeSkeleton.
         <param name="show_detailed_info" type="select" label="Show detailed info">
             <option value="no" selected="True">No</option>
             <option value="yes">Yes</option>
         </param>
-        <expand macro="max_heap_size_type_conditional" />
+        -->
     </inputs>
     <outputs>
         <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
@@ -63,9 +66,12 @@
             <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
         </test>
         <test>
+            <!-- TODO: Change this test and the following test to set "show_detailed_info"
+            to "yes" when the tool has been enhanced to use the future "Display labeled skeletons"
+            option.  See http://fiji.sc/AnalyzeSkeleton.  -->
             <param name="input" value="skeletonized_blobs.gif" />
             <param name="input_datatype" value="gif" />
-            <param name="show_detailed_info" value="yes" />
+            <!-- <param name="show_detailed_info" value="yes" /> -->
             <output name="output" file="detailed.tabular" ftype="tabular" />
         </test>
         <test>
@@ -73,7 +79,7 @@
             <param name="input_datatype" value="jpg" />
             <param name="prune_cycle_method" value="shortest_branch" />
             <param name="calculate_largest_shortest_path" value="yes" />
-            <param name="show_detailed_info" value="yes" />
+            <!-- <param name="show_detailed_info" value="yes" /> -->
             <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
         </test>
     </tests>
@@ -112,7 +118,6 @@
 - **Prune cycle method**: prune the possible loops in the skeleton.
 - **Prune ends**: prunes any branch that ends in an end-point.
 - **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path).
-- **Show detailed info**: produces information about the branches of each skeleton in the image.
 ]]>
     </help>
     <citations>