diff mz_to_sqlite.xml @ 3:c8bdcf574413 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864

--- a/mz_to_sqlite.xml	Fri Jun 17 15:03:22 2016 -0400
+++ b/mz_to_sqlite.xml	Mon Feb 11 17:30:12 2019 -0500
@@ -1,36 +1,47 @@
-<tool id="mz_to_sqlite" name="mz to sqlite" version="1.2.0">
+<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.2">
     <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="2.0.2">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>
+            <param name="mzinput" value="test_id.mzid" ftype="mzid"></param>
+            <param name="scanfiles" value="test.mgf" ftype="mgf"></param>
+            <param name="searchdbs" value="test.fasta" ftype="fasta"></param>
+            <output name="sqlite_db" file="sqlite.db" />
         </test>
     </tests>
     <help>
@@ -39,4 +50,5 @@
 
 ]]>
     </help>
+    <citations></citations>
 </tool>