Mercurial > repos > recetox > matchms_networking

diff matchms_networking.xml @ 6:9982b85ff4e7 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:28:13 +0000
parents 8147d93d372d
children d8e937f335b8
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--- a/matchms_networking.xml	Tue Jun 27 14:29:16 2023 +0000
+++ b/matchms_networking.xml	Thu Oct 12 13:28:13 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>create similarity network graph from matchms similarity scores</description>
 
     <macros>
@@ -16,15 +16,15 @@
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
 
+    <command detect_errors="aggressive"><![CDATA[
+        sh ${matchms_networking_cli}
+    ]]></command>
+
     <environment_variables>
         <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
         <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
     </environment_variables>
 
-    <command detect_errors="aggressive"><![CDATA[
-        sh ${matchms_networking_cli}
-    ]]></command>
-
     <configfiles>
         <configfile name="matchms_networking_cli">
             python3 ${__tool_directory__}/matchms_networking_wrapper.py \
@@ -78,7 +78,7 @@
     </inputs>
 
     <outputs>
-        <data label="Similarity network of ${scores.name}" name="similarity_network_file">
+        <data label="Similarity network of ${scores.name}" name="similarity_network_file" format="graphml">
             <change_format>
                 <when input="graph_format" value="graphml" format="graphml"/>
                 <when input="graph_format" value="cyjs" format="cyjs"/>