# HG changeset patch
# User galaxyp
# Date 1594217131 14400
# Node ID f5c632894818bda039f62e3efed8da6e4a3a99b5
# Parent  728d459bafe86dba0f0b53457901693198dd7e30
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 75b9f57bf0b41b2a0b1e1c9f73447a1125fc245e"

diff -r 728d459bafe8 -r f5c632894818 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Jul 08 10:05:31 2020 -0400
@@ -0,0 +1,19 @@
+# MzToSQLite
+
+## Description
+
+Parses MzIdentML, FASTA and MGF scan files into a SQLite3 database. The schema is used by MVPApplication in visualizing the parsed data.
+
+## General Requirements
+
+MzToSQLite is threaded during the read stages of processing. It is single threaded during SQL writes. It will perform best when given one core per MGF file. But it runs well with between two and four cores.
+
+Reading the MGF files is memory intensive, set the _JAVA_OPTIONS to the minimum recommended below.
+
+**Example Recommended Settings**
+
+    One core, minimum memory:
+        _JAVA_OPTIONS: -Xms20G -Xmx20G
+
+    Four core, slightly faster performance (performance determined by size of each MGF file):
+        _JAVA_OPTIONS: -Xms40G -Xmx40G
diff -r 728d459bafe8 -r f5c632894818 mz_to_sqlite.xml
--- a/mz_to_sqlite.xml	Mon Jun 29 17:06:00 2020 -0400
+++ b/mz_to_sqlite.xml	Wed Jul 08 10:05:31 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.4">
+<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.4+galaxy1">
     <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
     <requirements>
         <requirement type="package" version="2.0.4">mztosqlite</requirement>
@@ -8,7 +8,7 @@
     </stdio>
     <command>
         <![CDATA[
-mz_to_sqlite -Xms1g -Xmx6g 
+mz_to_sqlite
      -numthreads "\${GALAXY_SLOTS:-4}"
      -dbname 'sqlite.db'
      -mzid '$mzinput'