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Repository camera_annotate
Owner: lecorguille
Synopsis: [Metabolomics][W4M][LC-MS] CAMERA R Package - Annotation - Returns annotation results (isotope peaks, adducts and fragments)
Part of the W4M project: http://workflow4metabolomics.org CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html Wrapper script for automatic annotation of isotope peaks, adducts and fragments for a (grouped) xcmsSet xs. The function returns an xsAnnotate object. BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too
Galaxy wrapper repository: https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera_annotate
Type: unrestricted
Revision: 17:73d82de36369
This revision can be installed: True
Times cloned / installed: 954

Repository README files - may contain important installation or license information

Changelog/News -------------- **Version 2.2.4 - 09/10/2018** - NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job **Version 2.2.3 - 30/04/2018** - NEW: support the new xcms 3.0.0 wrapper **Version 2.2.2 - 01/03/2018** - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 **Version 2.2.1 - 29/11/2017** - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C **Version 2.2.0 - 03/02/2017** - BUGFIX: the diffreport ids didn't convert the rt in minute as the other export - UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata. - IMPROVEMENT: add some sections within the form to separate the different parts of the process - IMPROVEMENT: add the possibility to use defined ruleset - IMPROVEMENT: add the possibility to set the MZ digit within the identifiants - IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet **Version 2.1.5 - 21/04/2016** - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 **Version 2.1.4 - 18/04/2016** - TEST: refactoring to pass planemo test using conda dependencies **Version 2.1.3 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions) - IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf. - UPDATE: refactoring of internal management of inputs/outputs **VERSION 2.1.0 - 09/10/2015** - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) **VERSION 2.1.0 - 07/06/2015** - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. - IMPROVEMENT: parameter labels have changed to facilitate their reading. - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
Dependencies of this repository

Repository rdata_camera_datatypes revision 4a51ab3d8ecf owned by lecorguille
Repository rdata_xcms_datatypes revision 544f6d2329ac owned by lecorguille

Contents of this repository

Name Description Version Minimum Galaxy Version
CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 2.2.4 16.01

Categories
Metabolomics - Tools for use in the study of Metabolomics