- DIMSP for Galaxy
Galaxy tool for Direct-Infusion Mass Spectrometry (DIMS) based lipidomics -data processing and filtering.
-For details how to get annotation and peak table, see -dims_processing.
-- Installation
-
-
-
-
Install Galaxy under Linux.
-
- -
-
Install conda under -Linux.
-conda
is used to installrequirements
of this tool, i.e. R -packages used:optparse
,WriteXLS
,xcms
,data.table
, -reshape
,lattice
,impute
andpcaMethods
.
- -
-
Use
-git
to clone this tool-git clone https://github.com/wanchanglin/dimsp.git
- -
-
Add this tool's location into Galaxy' tool config file: -
-~/Galaxy/config/tool_conf.xml
. For example, one simplified -tool_conf.xml
looks like:-<?xml version='1.0' encoding='utf-8'?> -<toolbox monitor="true"> - - <section id="getext" name="Get Data"> - <tool file="data_source/upload.xml" /> - </section> - - <section id="MyTools" name="My Tools"> - <tool file="/path/to/dimsp/dimsp.xml" /> - <tool file="/path/to/dimsp/dimsp_filter.xml" /> - </section> - -</toolbox>
- -
-
Test data are in
-test-data
, includes:-
-
- mzXML and mzML files for DIMSP processing. -
- Lipid lists in TSV(Tab Separated Values) format. -
- TSV files for DIMSP filtering. -
-
- Authors, contributors & contacts
-
-
- Wanchang Lin (wl361@cam.ac.uk), University of Cambridge -
- Zoe Hall (zlh22@cam.ac.uk), University of Cambridge -
- Julian L Griffin (jlg40@cam.ac.uk), University of Cambridge -