# HG changeset patch # User metaboflow_cam # Date 1569314252 14400 # Node ID dada1f17021da3c1f2b49d670e258a1867569289 Uploaded diff -r 000000000000 -r dada1f17021d massPix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/massPix Tue Sep 24 04:37:32 2019 -0400 @@ -0,0 +1,1164 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GitHub - wanchanglin/massPix + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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TypeNameLatest commit messageCommit time
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+ + + + imzMLConverter + + + add java stuff + + + Apr 24, 2018 +
+ + + + libraries + + + initial + + + Apr 23, 2018 +
+ + + + test-data + + + pass all tests + + + Apr 6, 2019 +
+ + + + test + + + pass all tests + + + Apr 6, 2019 +
+ + + + .gitignore + + + add ibd file + + + Apr 3, 2019 +
+ + + + README.md + + + README.md and minor changes + + + Mar 28, 2019 +
+ + + + all_massPix.R + + + planemo test + + + Mar 25, 2019 +
+ + + + macros.xml + + + planemo test for new data + + + Apr 5, 2019 +
+ + + + massPix.R + + + planemo test and add 'set.seed' in R script + + + Apr 5, 2019 +
+ + + + massPix.xml + + + pass all tests + + + Apr 6, 2019 +
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+ + README.md +

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+

massPix for Galaxy

+

This is Galaxy tool for R package massPix which processes high resolution +mass spectrometry imaging data, performs multivariate statistics (PCA, +clustering) and lipid identification. For details, see +R package massPix and Metabolomics +publication.

+

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.

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    Use git to clone this tool

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    git clone https://github.com/wanchanglin/massPix.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:

    +
    <?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/massPix/massPix.xml" />
+  </section>
+
+</toolbox>
    +
    • +
  • +

    The Galaxy tool uses R packages optparse, +WriteXLS, calibrate and rJava. This tool embeds a modified +massPix package for Galaxy only.

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    To test the tool, use data inside test-data or download test data (.ibd +and .imzML files) from the +MetaboLights repository accession +number MTBLS487.

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+

Authors, contributors & contacts

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