--- a/blasttoolssearch/blasttoolssearch.xml	Wed Jul 19 06:45:26 2023 +0000
+++ b/blasttoolssearch/blasttoolssearch.xml	Wed Jul 19 10:18:30 2023 +0000
@@ -1,4 +1,4 @@
-<tool name="blasttoolssearch" id="blasttoolssearch" version="3.0">
+<tool name="blasttoolssearch" id="blasttoolssearch" version="3.1">
   <!--Source in git at: https://github.com/fubar2/galaxy-->
   <!--Created by toolfactory@galaxy.org at 19/07/2023 12:39:19 using the Galaxy Tool Factory.-->
   <description>Runs a legacy Java jar called blasttools from https://github.com/schmidda/blast-tools/tree/master</description>
@@ -10,11 +10,12 @@
     <exit_code range="1:" level="fatal"/>
   </stdio>
   <version_command><![CDATA[echo "3.0"]]></version_command>
-  <command><![CDATA[bash
-$runme
-$blastn_search_outputs
-$__tool_directory__/BlastTools.jar
-$summary_viruses_viroids
+  <command><![CDATA[
+mkdir -p files &&
+#for afile in $blastn_search_outputs:
+ln -sf '$afile' files/\$(basename '$afile') &&
+#end for
+bash $runme ./files $__tool_directory__/BlastTools.jar $summary_viruses_viroids
 ]]></command>
   <configfiles>
     <configfile name="runme"><![CDATA[#raw
@@ -35,8 +36,8 @@
 # The script will Look for all files with the suffix *.tabular
 
 #Processing tabular files
-file=$1
-
+for file in files/*.*
+  do
     var=$(basename $file)
 
     #STEP0: fetch Top 1 Hits
@@ -75,11 +76,11 @@
     cat summary_${var}.txt | head -1 > header
     #report 1
     cat header ${var}_filtered.txt > $3
-
+done
 #end raw]]></configfile>
   </configfiles>
   <inputs>
-    <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="false"/>
+    <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="true"/>
   </inputs>
   <outputs>
     <data name="summary_viruses_viroids" format="tabular" label="summary_viruses_viroids" hidden="false"/>