Mercurial > repos > galaxyp > mz_to_sqlite
changeset 4:f5c632894818 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 75b9f57bf0b41b2a0b1e1c9f73447a1125fc245e"
| author | galaxyp |
|---|---|
| date | Wed, 08 Jul 2020 10:05:31 -0400 |
| parents | 728d459bafe8 |
| children | 8190f6083c0d |
| files | README.md mz_to_sqlite.xml |
| diffstat | 2 files changed, 21 insertions(+), 2 deletions(-) [+] |
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--- /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
--- 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'