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1 LC/MS matching
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2 ==============
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4 [![Build Status](https://travis-ci.org/workflow4metabolomics/lcmsmatching.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/lcmsmatching)
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6 An LC/MS matching tool for [Galaxy](https://galaxyproject.org/), part of the [Workflow4Metabolomics](http://workflow4metabolomics.org/) project, and developed during the [MetaboHUB](http://www.metabohub.fr/en) project.
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8 The two matching algorithms used in this tool have been imported from developments made at [CEA](http://www.cea.fr/english) Saclay, inside the *DSV/IBITEC-S/SPI*. They have been translated from C# to R.
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10 For more information, see the galaxy tool page, help section, available inside `galaxy/lcmsmatching.xml`.
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12 ## lcmsmatching script
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14 This is the script, included in this repository, that allows to run on command line an MZ matching on one of the available database types.
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16 Please run `lcmsmatching -h` for a help page listing all options and presenting some examples.
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18 ## Dependencies
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20 * `R` version `3.5.1`.
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21 * `R` packages:
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22 - `getopt` >= `1.20.0`.
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23 - `biodb` >= `1.2.0rc2`.
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25 ## Changelog
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27 ### 4.0.2
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29 * Increase getopt version to 1.20.2.
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31 ### 4.0.1
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33 * Downgrade to Galaxy 18.05. Test in both 18.05 and 18.09.
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35 ### 4.0.0
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37 * Switch to biodb R library (<http://github.com/pkrog/biodb>).
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38 * Remove Excel and 4TabSql databases from script.
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39 * Remove all dynamic fields in XML (i.e.: fields computed using python scripts, like the list of chromatogaphic columns).
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40 * Use now a single field for in-house file databases column names, whose value is a comma separated list of key/value pairs.
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41 * Update Peakforest URL.
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43 ### 3.4.3
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45 * Returns empty match in case of NA values in mz.low and mz.high.
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46 * Speed up HTML output writing.
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48 ### 3.3.1
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50 * Correct a bug while trying to connect to Peakforest for getting the list of chromatographic columns.
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52 ### 3.3.0
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54 * The file database (in-house) field names are now presented in individual choice lists instead of a single text box where you had to insert a very long keys/values string.
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55 * The tool now tries to guess the names of the file database fields, the values of the MS mode column, and the names of the input file columns.
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56 * Allows to select the unit (minutes or seconds) of retention time values inside the input file, but also inside the file database (in-house).