# HG changeset patch # User metaboflow_cam # Date 1571730565 14400 # Node ID b8b3148de013e513040cc531bb23f26b11148528 # Parent 77457f03804ac9549d8b7440c89cc1ca67e18bb1 Deleted selected files diff -r 77457f03804a -r b8b3148de013 dimsp --- a/dimsp Tue Oct 22 03:48:52 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1174 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GitHub - wanchanglin/dimsp - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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- - wanchanglin - - - - - - planemo test again - -
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- - - - test-data - - - planemo test again - - - Oct 11, 2019 -
- - - - test - - - remove large mzXML test files and pass planemo tests - - - Oct 6, 2019 -
- - - - .gitignore - - - planemo test again - - - Oct 11, 2019 -
- - - - README.md - - - debug RSD threshold for QC filtering and pass all 'planemo test' - - - Apr 1, 2019 -
- - - - all_dimsp.R - - - tidy up and add mzML input - - - Mar 1, 2019 -
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- - - - dimsp_filter.R - - - debug RSD threshold for QC filtering and pass all 'planemo test' - - - Apr 1, 2019 -
- - - - dimsp_filter.xml - - - remove large mzXML test files and pass planemo tests - - - Oct 6, 2019 -
- - - - fs_filter.R - - - tidy up and add mzML input - - - Mar 1, 2019 -
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- - README.md -

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DIMSP for Galaxy

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Galaxy tool for Direct-Infusion Mass Spectrometry (DIMS) based lipidomics -data processing and filtering.

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For details how to get annotation and peak table, see -dims_processing.

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Installation

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    Install Galaxy under Linux.

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    Install conda under -Linux. conda is used to install requirements of this tool, i.e. R -packages used: optparse, WriteXLS, xcms, data.table, -reshape, lattice, impute and pcaMethods.

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    Use git to clone this tool

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    git clone https://github.com/wanchanglin/dimsp.git
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    Add this tool's location into Galaxy' tool config file: -~/Galaxy/config/tool_conf.xml. For example, one simplified -tool_conf.xml looks like:

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    <?xml version='1.0' encoding='utf-8'?>
-<toolbox monitor="true">
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-  <section id="getext" name="Get Data">
-    <tool file="data_source/upload.xml" />
-  </section>
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-  <section id="MyTools" name="My Tools">
-    <tool file="/path/to/dimsp/dimsp.xml" />
-    <tool file="/path/to/dimsp/dimsp_filter.xml" />
-  </section>
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-</toolbox>
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    Test data are in test-data, includes:

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    • mzXML and mzML files for DIMSP processing.
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    • Lipid lists in TSV(Tab Separated Values) format.
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    • TSV files for DIMSP filtering.
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Authors, contributors & contacts

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