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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce
author prog
date Sun, 09 Apr 2017 10:44:21 -0400
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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 ## search-mz
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14 This is the script, included in this repository, that allows run on command line an MZ matching on one of the available database types.
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16 Please run `search-mz -h` for a help page listing all options and presenting some examples.
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18 ## Dependencies
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20 * `libssl-dev`.
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21 * `libcurl4-openssl-dev`.
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22 * `libxml2-dev`.
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23 * `R` version `3.2.2`.
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24 * `R` packages:
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25 - `getopt` >= `1.20.0`.
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26 - `stringr` >= `1.0.0`.
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27 - `plyr` >= `1.8.3`.
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28 - `XML` >= `3.98`.
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29 - `bitops` >= `1.0_6`.
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30 - `RCurl` >= `1.95`.
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31 - `jsonlite` >= `1.1`.
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33 ## Updates
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35 ### 3.3.1
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37 * Correct a bug while trying to connect to Peakforest for getting the list of chromatographic columns.
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39 ### 3.3.0
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41 * 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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42 * 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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43 * Allows to select the unit (minutes or seconds) of retention time values inside the input file, but also inside the file database (in-house).