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author prog
date Fri, 22 Feb 2019 16:04:22 -0500
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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. 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`. 10 For more information, see the galaxy tool page, help section, available inside `galaxy/lcmsmatching.xml`.
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12 ## search-mz 12 ## lcmsmatching script
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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. 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 `search-mz -h` for a help page listing all options and presenting some examples. 16 Please run `lcmsmatching -h` for a help page listing all options and presenting some examples.
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18 ## Dependencies 18 ## Dependencies
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20 * `libssl-dev`. 20 * `R` version `3.5.1`.
21 * `libcurl4-openssl-dev`.
22 * `libxml2-dev`.
23 * `R` version `3.2.2`.
24 * `R` packages: 21 * `R` packages:
25 - `getopt` >= `1.20.0`. 22 - `getopt` >= `1.20.0`.
26 - `stringr` >= `1.0.0`. 23 - `biodb` >= `1.2.0rc2`.
27 - `plyr` >= `1.8.3`.
28 - `XML` >= `3.98`.
29 - `bitops` >= `1.0_6`.
30 - `RCurl` >= `1.95`.
31 - `jsonlite` >= `1.1`.
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33 ## Updates 25 ## Changelog
26
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>).
38 * Remove Excel and 4TabSql databases from script.
39 * Remove all dynamic fields in XML (i.e.: fields computed using python scripts, like the list of chromatogaphic columns).
40 * Use now a single field for in-house file databases column names, whose value is a comma separated list of key/value pairs.
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.
46 * Speed up HTML output writing.
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35 ### 3.3.1 48 ### 3.3.1
36 49
37 * Correct a bug while trying to connect to Peakforest for getting the list of chromatographic columns. 50 * Correct a bug while trying to connect to Peakforest for getting the list of chromatographic columns.
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