# HG changeset patch # User computational-metabolomics # Date 1586456925 14400 # Node ID cad0376c0b66ceb61f6520ca3e3baaf91a2512f0 # Parent e94e94d8441f99ed7918e487e68b9191d2c8e8a7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459" diff -r e94e94d8441f -r cad0376c0b66 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Apr 09 14:28:45 2020 -0400 @@ -0,0 +1,154 @@ +msPurity for Galaxy +======================== +|Build Status (Travis)| |Git| |Bioconda| |License| + + +Version v1.12.2+galaxy1 +------ + + - msPurity + - bioconductor-mspurity v1.12.2 + - Galaxy tools + - v1 + +About +------ +Galaxy tools for the Bioconductor R package msPurity. Tools available for assessing precursor ion purity of +LC-MS/MS or DI-M/MS data that has been acquired. And tools are available to assess LC-MS or DI-MS for +anticipated precursor ion purity to guide a later fragmentation experiment. + +Additional, tools available to perform LC-MS/MS spectral matching. + +Associated paper `msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics. Analytical Chemistry `_ + +Use the following links for more details of the msPurity R package: + +* Bioconductor: http://bioconductor.org/packages/msPurity/ +* Vignette: https://bioconductor.org/packages/devel/bioc/vignettes/msPurity/inst/doc/msPurity-vignette.html +* Manual: http://bioconductor.org/packages/devel/bioc/manuals/msPurity/man/msPurity.pdf +* Bioconductor mirror code: https://github.com/Bioconductor-mirror/msPurity +* Github code: https://github.com/computational-metabolomics/mspurity +* Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity +* Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity + + + + +Dependencies +------ +Dependencies for these Galaxy tools should be handled by CONDA. The most recent version of the msPurity R package can found on channel `tomnl `_ on `anaconda `_. Warning this will be a different version of the package compared to the BICONDA bioconductor-mspurity. + + +Galaxy +------ +`Galaxy `_ is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. + + +Authors, contributors & contacts +------------------------- + +- Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) `_ +- Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) `_ +- Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) `_ +- Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) `_ +- Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) `_ + +Changes +------------------------- +v1.12.2-galaxy1 + - grpPeaklist reference incorrect in createDatabase.xml + - Add custom adduct handling for createMSP + - Change output of flagRemove to tabular + + +v1.12.2-galaxy0 + - Update to version v1.12.2 of `msPurity `_ + - Optional summary output for combineAnnotations (for very large output) + - Extra column added to flagRemove output + - Hide probmetab input + - Make dimsPredictPuritySingle more compatible with "simple workflow inputs" + + +v1.12.1-galaxy0 + - Update to version v1.12.1 of `msPurity `_ + +v1.12.0-galaxy1 + - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne + - Exit script without error for flagRemove + - Username updated in Toolshed yaml + +v1.12.0-galaxy0 + - Updates for Bioconductor stable msPurity v1.12.0 release + - Additional columns added for spectral matching (for msnpy use case) + - Merge of v1.11.4-galaxy1 + +v1.11.4-galaxy1 + - Not submitted to toolshed + - Update to follow IUC guidelines for Galaxy tool development + +v1.11.4-galaxy0.2.7 + - submitted to test toolshed (20190927) + - Bug fix for spectralMatching choice of instrument types + +v1.11.4-galaxy0.2.6: + - submitted to test toolshed (20190924) + - Bug fix for createAnnotation database local path + - Update of instrument types for spectral matching + - Update of split_msp tool to handle different MSP types + + +v1.11.4-galaxy0.2.5: + - submitted to test toolshed (20190913) + - Added ppmInterp parameter to purityA + - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database + - Update of spectralMatching tool to use either sqlite, postgres or mysql database + - Added include_adducts parameter to createMSP + +v1.11.3-galaxy0.2.5: + - Note: This was not pushed to test toolshed + - Clean up of the versioning to be in line with IUC + - All tools updated with the same versioning + - Bump to msPurity v1.11.3 to so EIC is calculated for all features + +v0.2.5 (spectralMatching): + - spectralMatching - Extra details from matched library spectra is now added to the database (fix) + +v0.2.4 (all tools): + - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data + +v0.2.2 (spectralMatching): + - spectralMatching - Extra details from matched library spectra is now added to the database + +v0.2.3 (createDatabase): + - createDatabase.xml fix for EIC creation + +v0.2.2 (createDatabase, flagRemove, combineAnnotation): + - createDatabase.xml fix for xcms3 and CAMERA + - flagRemove xcms3 fix + - combineAnnotation Made sirius, probmetab and metfrag optional + - combineAnnotation fix column sirius + +v0.2.1 (all tools): + - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase) + +v0.2.0 (all tools): + - Update all tools to be more consistent with msPurity core code + +License +------- +Released under the GNU General Public License v3.0 (see `LICENSE file `_) + + +.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI + :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy + +.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600 + :target: https://github.com/computational-metabolomics/mspurity-galaxy + +.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600 + :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html + +.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg + :target: https://www.gnu.org/licenses/gpl-3.0.html + + diff -r e94e94d8441f -r cad0376c0b66 createMSP.R --- a/createMSP.R Wed Apr 01 11:19:15 2020 -0400 +++ b/createMSP.R Thu Apr 09 14:28:45 2020 -0400 @@ -15,6 +15,7 @@ make_option("--intensity_ra",type="character"), make_option("--include_adducts",type="character"), make_option("--msp_schema",type="character"), + make_option("--include_adducts_custom",type="character", default=""), make_option("--out_dir",type="character", default=".") ) opt <- parse_args(OptionParser(option_list=option_list)) @@ -66,17 +67,33 @@ xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]]) } + + + + +if (is.null(opt$include_adducts_custom)){ + include_adducts_custom <- '' +}else{ + include_adducts_custom <- opt$include_adducts_custom +} + + if (opt$include_adducts=='None'){ include_adducts <- '' }else{ include_adducts <- opt$include_adducts - include_adducts <- gsub("__ob__", "[", include_adducts) - include_adducts <- gsub("__cb__", "]", include_adducts) - include_adducts <- trimws(include_adducts) +} + +include_adducts_all <- paste(include_adducts_custom, ',', include_adducts, sep="") - include_adducts <- gsub(",", " ", include_adducts) +include_adducts_all <- gsub("^,", "", include_adducts_all) +include_adducts_all <- gsub(",$", "", include_adducts_all) -} +include_adducts_all <- gsub("__ob__", "[", include_adducts_all) +include_adducts_all <- gsub("__cb__", "]", include_adducts_all) +include_adducts_all <- trimws(include_adducts_all) +include_adducts_all <- gsub(",", " ", include_adducts_all) + if(is.null(opt$filter)){ @@ -96,7 +113,7 @@ xcms_groupids = xcms_groupids, filter = filter, intensity_ra=opt$intensity_ra, - include_adducts=include_adducts, + include_adducts=include_adducts_all, msp_schema=opt$msp_schema) print('msp created') diff -r e94e94d8441f -r cad0376c0b66 macros.xml --- a/macros.xml Wed Apr 01 11:19:15 2020 -0400 +++ b/macros.xml Thu Apr 09 14:28:45 2020 -0400 @@ -1,7 +1,7 @@ 1.12.2 - 0 + 1 @@ -16,6 +16,9 @@ + + [A-Za-z0-9,\[\] \+\-]+ +