# HG changeset patch
# User galaxyp
# Date 1594217013 0
# Node ID 9a1ced29b1301ae226467e7e1cd1dbd8d03fbc58
# Parent  2a8a9f07782eca4d2e70d8e35a83415b3456b85e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 75b9f57bf0b41b2a0b1e1c9f73447a1125fc245e"

diff -r 2a8a9f07782e -r 9a1ced29b130 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Jul 08 14:03:33 2020 +0000
@@ -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 2a8a9f07782e -r 9a1ced29b130 mz_to_sqlite.xml
--- a/mz_to_sqlite.xml	Mon Jun 29 21:05:40 2020 +0000
+++ b/mz_to_sqlite.xml	Wed Jul 08 14:03:33 2020 +0000
@@ -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'