Mercurial > repos > iuc > humann2_join_tables

changeset 4:bc070e7154de draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
author iuc
date Fri, 05 Feb 2021 18:17:35 +0000
parents edb2b396611d
children 75e67c9b02ee
files humann2_join_tables.xml humann2_macros.xml repository_dependencies.xml
diffstat 3 files changed, 11 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/humann2_join_tables.xml	Fri Jun 19 11:39:40 2020 +0000
+++ b/humann2_join_tables.xml	Fri Feb 05 18:17:35 2021 +0000
@@ -1,8 +1,9 @@
-<tool id="humann2_join_tables" name="Join" version="@WRAPPER_VERSION@.1">
+<tool id="humann2_join_tables" name="Join" version="@WRAPPER_VERSION@.2">
     <description>HUMAnN2 generated tables</description>
     <macros>
         <import>humann2_macros.xml</import>
     </macros>
+    <expand macro="stdio"/>
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
--- a/humann2_macros.xml	Fri Jun 19 11:39:40 2020 +0000
+++ b/humann2_macros.xml	Fri Feb 05 18:17:35 2021 +0000
@@ -7,6 +7,13 @@
             <yield/>
         </requirements>
     </xml>
+    
+    <xml name="stdio">
+        <stdio>
+            <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" description="Out of memory error occurred" />
+            <regex match="MemoryError" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
+        </stdio>
+    </xml>
     <xml name="version">
         <version_command>humann2 --version</version_command>
     </xml>
--- a/repository_dependencies.xml	Fri Jun 19 11:39:40 2020 +0000
+++ b/repository_dependencies.xml	Fri Feb 05 18:17:35 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
 <repositories description="This requires the HUMAnN2 data manager definition to install all required databases.">
-    <repository changeset_revision="db1dd1044a39" name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
-    <repository changeset_revision="afe83ae43e1e" name="data_manager_humann2_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+    <repository name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="db1dd1044a39"/>
+    <repository name="data_manager_humann2_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="afe83ae43e1e"/>
 </repositories>
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