Mercurial > repos > prog > lcmsmatching
comparison README.md @ 5:fb9c0409d85c draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce
| author | prog |
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| date | Wed, 19 Apr 2017 10:00:05 -0400 |
| parents | |
| children | f86fec07f392 |
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| 1 LC/MS matching | |
| 2 ============== | |
| 3 | |
| 4 [](https://travis-ci.org/workflow4metabolomics/lcmsmatching) | |
| 5 | |
| 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. | |
| 7 | |
| 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. | |
| 9 | |
| 10 For more information, see the galaxy tool page, help section, available inside `galaxy/lcmsmatching.xml`. | |
| 11 | |
| 12 ## search-mz | |
| 13 | |
| 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. | |
| 15 | |
| 16 Please run `search-mz -h` for a help page listing all options and presenting some examples. | |
| 17 | |
| 18 ## Dependencies | |
| 19 | |
| 20 * `libssl-dev`. | |
| 21 * `libcurl4-openssl-dev`. | |
| 22 * `libxml2-dev`. | |
| 23 * `R` version `3.2.2`. | |
| 24 * `R` packages: | |
| 25 - `getopt` >= `1.20.0`. | |
| 26 - `stringr` >= `1.0.0`. | |
| 27 - `plyr` >= `1.8.3`. | |
| 28 - `XML` >= `3.98`. | |
| 29 - `bitops` >= `1.0_6`. | |
| 30 - `RCurl` >= `1.95`. | |
| 31 - `jsonlite` >= `1.1`. | |
| 32 | |
| 33 ## Updates | |
| 34 | |
| 35 ### 3.3.1 | |
| 36 | |
| 37 * Correct a bug while trying to connect to Peakforest for getting the list of chromatographic columns. | |
| 38 | |
| 39 ### 3.3.0 | |
| 40 | |
| 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. | |
| 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. | |
| 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). |