--- a/mz_to_sqlite.xml	Fri Jun 17 15:13:02 2016 -0400
+++ b/mz_to_sqlite.xml	Wed Mar 28 09:33:18 2018 -0400
@@ -1,33 +1,40 @@
-<tool id="mz_to_sqlite" name="mz to sqlite" version="1.2.0">
+<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.0">
     <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
     <requirements>
-      <requirement type="package" version="1.2.0">mztosqlite</requirement>
+      <requirement type="package" version="2.0.0">mztosqlite</requirement>
     </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error Running mz_to_sqlite" />
    </stdio>
     <command>
 <![CDATA[
-java -jar \$MZTOSQLITE_JAR_PATH -s $mzsqlite 
-#if len($scanfiles) > 0:
-$scanfiles.__str__.replace(',',' ') 
-#end if
-#if len($searchdbs) > 0:
-$searchdbs.__str__.replace(',',' ') 
-#end if
-#if len($mzinputs) > 0:
-$mzinputs.__str__.replace(',',' ')
-#end if
+mz_to_sqlite -Xms1g -Xmx6g 
+     -numthreads "\${GALAXY_SLOTS:-4}"
+     -dbname 'sqlite.db'
+     -mzid '$mzinput'
+     #if len($scanfiles) > 0:
+     #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')])
+     -scanfiles $files
+     #set $dfiles = [a for a in $scanfiles]
+     -scanFilesDisplayName 
+          #for $f in $dfiles
+          '$f.display_name'  
+          #end for
+     #end if
+     #if len($searchdbs) > 0:
+     #set $dbFiles =  " ".join(["'"+ a.strip() + "'" for a in str($searchdbs).split(',')])
+     -fasta $dbFiles
+     #end if
 ]]>
     </command>
     <inputs>
-        <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/>
+        <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/>
         <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/>
         <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta"
                help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
     </inputs>
     <outputs>
-        <data format="mz.sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/>
+        <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/>
     </outputs>
     <tests>
         <test>