Mercurial > repos > goeckslab > mesmer

changeset 1:02abff468d60 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 374e4528db4e3ce7984e2ed2c2bae55c19c17371
author goeckslab
date Thu, 10 Nov 2022 20:38:34 +0000
parents 53240d7c1fc5
children 187918c47051
files macros.xml mesmer.xml
diffstat 2 files changed, 24 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Sep 08 15:17:30 2022 +0000
+++ b/macros.xml	Thu Nov 10 20:38:34 2022 +0000
@@ -5,7 +5,26 @@
             <container type="docker">quay.io/goeckslab/mesmer:@TOOL_VERSION@</container>
         </requirements>
     </xml>
-
+    <xml name="stdio">
+        <stdio>
+            <regex match="MemoryError"
+               source="both"
+               level="fatal_oom"
+               description="Out of Memory" />
+            <regex match="std::bad_alloc"
+               source="both"
+               level="fatal_oom"
+               description="Out of Memory" />
+            <regex match="java.lang.OutOfMemoryError"
+               source="both"
+               level="fatal_oom"
+               description="Out of Memory" />
+            <regex match="Out of memory"
+               source="both"
+               level="fatal_oom"
+               description="Out of Memory" />
+        </stdio>
+    </xml>
     <xml name="version_cmd">
         <version_command>@CMD_BEGIN@ --help</version_command>
     </xml>
@@ -16,6 +35,6 @@
     </xml>
 
     <token name="@TOOL_VERSION@">0.3.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@CMD_BEGIN@">python /usr/src/app/run_app.py mesmer</token>
 </macros>
--- a/mesmer.xml	Thu Sep 08 15:17:30 2022 +0000
+++ b/mesmer.xml	Thu Nov 10 20:38:34 2022 +0000
@@ -6,6 +6,7 @@
     </macros>
 
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_cmd"/>
 
     <command detect_errors="exit_code"><![CDATA[
@@ -53,8 +54,8 @@
         <test>
             <param name="nuclear_image" value="test.tiff" />
             <param name="compartment" value="nuclear" />
-            <param name="membrane_select.membrane_segment" value="False" />
-            <param name="image_mmp" value="0.65" />
+            <param name="membrane_segment" value="False" />
+            <param name="image_mpp" value="0.65" />
             <param name="squeeze" value="--squeeze" />
             <output name="mask" ftype="tiff">
                 <assert_contents>