Mercurial > repos > perssond > s3segmenter

diff macros.xml @ 2:96d0d969ebc9 draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/s3segmenter commit 0f4f17235c5961c2fd3d4c30180507f66214c11d
author goeckslab
date Fri, 16 Sep 2022 20:05:54 +0000
parents 41e8efe8df43
children
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line diff
--- a/macros.xml	Fri Mar 11 23:37:49 2022 +0000
+++ b/macros.xml	Fri Sep 16 20:05:54 2022 +0000
@@ -2,25 +2,36 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <container type="docker">labsyspharm/s3segmenter:@VERSION@</container>
+            <!--
             <requirement type="package" version="3.7">python</requirement>
             <requirement type="package">scikit-learn</requirement>
             <requirement version="0.14.2" type="package">scikit-image</requirement>
             <requirement type="package">matplotlib</requirement>
             <requirement version="2021.6.6" type="package">tifffile</requirement>
             <requirement type="package">opencv</requirement>
-            <!-- <requirement type="package">ome_types</requirement> -->
+            -->  
+            <container type="docker">labsyspharm/s3segmenter:@TOOL_VERSION@</container>
         </requirements>
     </xml>
 
-    <xml name="version_cmd">
-        <version_command>echo @VERSION@</version_command>
-    </xml>
     <xml name="citations">
         <citations>
         </citations>
     </xml>
 
-    <token name="@VERSION@">1.3.12</token>
-    <token name="@CMD_BEGIN@">python3 $__tool_directory__/S3segmenter.py</token>
+    <token name="@TOOL_VERSION@">1.3.12</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">19.01</token>
+    <token name="@CMD_BEGIN@"><![CDATA[
+        S3SEG_CMD="" &&
+        if [ -f "/app/S3segmenter.py" ]; then
+            export S3SEG_CMD="python /app/S3segmenter.py";
+            export PYTHONPATH="/app";
+        else
+            export S3SEG_CMD="S3segmenter.py";
+        fi &&
+    ]]></token>
+    <xml name="version_cmd">
+        <version_command>@CMD_BEGIN@ $S3SEG_CMD --help</version_command>
+    </xml>
 </macros>