Mercurial > repos > recetox > xmsannotator_advanced

changeset 7:53246490912c draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit b99706e26938905c4d75763e3041f69fba4bff71"
author recetox
date Fri, 26 Feb 2021 09:05:21 +0000
parents fff8d90068cd
children fbe3edd0a06e
files xmsannotator_advanced.xml xmsannotator_macros.xml
diffstat 2 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/xmsannotator_advanced.xml	Tue Feb 23 12:55:20 2021 +0000
+++ b/xmsannotator_advanced.xml	Fri Feb 26 09:05:21 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy3">
+<tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy4">
     <macros>
         <import>xmsannotator_macros.xml</import>
     </macros>
@@ -8,7 +8,7 @@
     </requirements>
 
     <command detect_errors="aggressive"><![CDATA[
-        Rscript $wrapper
+        Rscript -e "n_workers <- \${GALAXY_SLOTS:-1}" -e "source('${wrapper}')"
     ]]></command>
 
     <configfiles>
@@ -36,7 +36,7 @@
                 boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds}"),
             #end if
                 redundancy_filtering = $scoring.redundancy_filtering,
-                n_workers = \${GALAXY_SLOTS:-1}
+                n_workers = n_workers
             )
 
             save_parquet(data = annotation, file = "${annotation_parquet}")
--- a/xmsannotator_macros.xml	Tue Feb 23 12:55:20 2021 +0000
+++ b/xmsannotator_macros.xml	Fri Feb 26 09:05:21 2021 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.2</token>
-    <token name="@DOCKER_IMAGE@">recetox/xmsannotator:1.3.2-recetox2</token>
+    <token name="@DOCKER_IMAGE@">recetox/xmsannotator:1.3.2-recetox3</token>
 
     <xml name="inputs">
         <param name="peak_table" type="data" format="csv,h5,parquet">