Mercurial > repos > imgteam > imagej2_analyze_skeleton

diff imagej2_analyze_skeleton.xml @ 1:3272e0439968 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:52:29 +0000
parents bb84f130a4e1
children bdee06a1bcfa
line wrap: on
line diff
--- a/imagej2_analyze_skeleton.xml	Tue Sep 17 17:04:59 2019 -0400
+++ b/imagej2_analyze_skeleton.xml	Mon Sep 28 16:52:29 2020 +0000
@@ -1,27 +1,33 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <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
-    ##TODO: seel below--show_detailed_info $show_detailed_info
-    --jython_script $__tool_directory__/imagej2_analyze_skeleton_jython_script.py
-    --output "$output"
-]]>
-    </command>
+    <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, $input.ext])
+ln -s '$input.file_name' '$input_with_ext' &&
+ImageJ --ij2 --headless --debug
+--jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py'
+'$error_log'
+'$input_with_ext'
+'$black_background'
+'$prune_cycle_method'
+'$prune_ends'
+'$calculate_largest_shortest_path'
+'no'
+'$output'
+&>'$error_log';
+if [[ $? -ne 0 ]]; then
+    cat '$error_log' >&2;
+fi
+]]></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" />
+        <expand macro="param_input"/>
+        <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>
@@ -45,42 +51,28 @@
         -->
     </inputs>
     <outputs>
-        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="output" format="tabular"/>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="skeletonized_blobs.gif" />
-            <param name="input_datatype" value="gif" />
-            <output name="output" file="basic.tabular" ftype="tabular" />
+            <param name="input" value="skeletonized_blobs.gif"/>
+            <output name="output" file="basic.tabular" ftype="tabular"/>
         </test>
         <test>
-            <param name="input" value="skeletonized_clown.jpg" />
-            <param name="input_datatype" value="jpg" />
-            <param name="prune_cycle_method" value="shortest_branch" />
-            <output name="output" file="shortest_branch_basic.tabular" ftype="tabular" />
+            <param name="input" value="skeletonized_clown.jpg"/>
+            <param name="prune_cycle_method" value="shortest_branch"/>
+            <output name="output" file="shortest_branch_basic.tabular" ftype="tabular"/>
         </test>
         <test>
-            <param name="input" value="skeletonized_blobs.gif" />
-            <param name="input_datatype" value="gif" />
-            <param name="calculate_largest_shortest_path" value="yes" />
-            <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
+            <param name="input" value="skeletonized_blobs.gif"/>
+            <param name="calculate_largest_shortest_path" value="yes"/>
+            <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" /> -->
-            <output name="output" file="detailed.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="input" value="skeletonized_clown.jpg" />
-            <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" /> -->
-            <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
+            <param name="input" value="skeletonized_clown.jpg"/>
+            <param name="prune_cycle_method" value="shortest_branch"/>
+            <param name="calculate_largest_shortest_path" value="yes"/>
+            <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular"/>
         </test>
     </tests>
     <help>