# HG changeset patch # User metaboflow_cam # Date 1569314346 14400 # Node ID 71f7501b302eddbf259ee0f2fb0690170c3220e6 # Parent dada1f17021da3c1f2b49d670e258a1867569289 Deleted selected files diff -r dada1f17021d -r 71f7501b302e massPix --- a/massPix Tue Sep 24 04:37:32 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1164 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GitHub - wanchanglin/massPix - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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- - - - imzMLConverter - - - add java stuff - - - Apr 24, 2018 -
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- - - - 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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massPix for Galaxy

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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.

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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.

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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:

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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/massPix/massPix.xml" />
-  </section>
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-</toolbox>
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    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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