# HG changeset patch # User metaboflow_cam # Date 1571730532 14400 # Node ID 77457f03804ac9549d8b7440c89cc1ca67e18bb1 Uploaded diff -r 000000000000 -r 77457f03804a dimsp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dimsp Tue Oct 22 03:48:52 2019 -0400 @@ -0,0 +1,1174 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GitHub - wanchanglin/dimsp + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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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 +
+ + + + dimsp.R + + + more comments on dimsp.R + + + Jul 19, 2019 +
+ + + + dimsp.xml + + + remove large mzXML test files and pass planemo tests + + + Oct 6, 2019 +
+ + + + 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 +
+ + + + macros.xml + + + add version in macro.xml + + + Oct 2, 2019 +
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+ + README.md +

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+ + +
+

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 install requirements of this tool, i.e. R +packages used: optparse, WriteXLS, xcms, data.table, +reshape, lattice, impute and pcaMethods.

    +
    • +
  • +

    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

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