Mercurial > repos > computational-metabolomics > mspurity_createmsp
changeset 3:2e8e367c4937 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
| author | computational-metabolomics |
|---|---|
| date | Thu, 09 Apr 2020 14:18:48 -0400 |
| parents | 54593159627d |
| children | 196f363638ca |
| files | README.rst createMSP.R createMSP.xml macros.xml test-data/createMSP_output_av_all_metadata_custom_adducts.msp |
| diffstat | 5 files changed, 314 insertions(+), 9 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Apr 09 14:18:48 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 <http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358>`_ + +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 <https://anaconda.org/tomnl/bioconductor-mspurity>`_ on `anaconda <https://anaconda.org/tomnl/bioconductor-mspurity>`_. Warning this will be a different version of the package compared to the BICONDA bioconductor-mspurity. + + +Galaxy +------ +`Galaxy <https://galaxyproject.org>`_ 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) <http://www.birmingham.ac.uk/index.aspx>`_ +- Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ +- Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) <http://www.urv.cat/en/>`_ +- Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_ +- Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_ + +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 <https://github.com/computational-metabolomics/msPurity/pull/71>`_ + - 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 <https://github.com/computational-metabolomics/msPurity/pull/71>`_ + +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 <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_) + + +.. |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 + +
--- a/createMSP.R Wed Apr 01 11:07:26 2020 -0400 +++ b/createMSP.R Thu Apr 09 14:18:48 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')
--- a/createMSP.xml Wed Apr 01 11:07:26 2020 -0400 +++ b/createMSP.xml Thu Apr 09 14:18:48 2020 -0400 @@ -27,6 +27,9 @@ --msp_schema $msp_schema --intensity_ra $intensity_ra --include_adducts $include_adducts + #if $include_adducts_custom + --include_adducts_custom "$include_adducts_custom" + #end if --out_dir '.' ]]></command> @@ -106,8 +109,13 @@ <option value="[M+CH3COO]-" >[M+CH3COO]-</option> <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option> </param> + <param argument="--include_adducts_custom" type="text" label="Always include the following custom adducts" + help="Additional custom adducts to include, should be comma separated" optional="true"> + <expand macro="text-adduct-regex-validator"/> + </param> + <param argument="--adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?" - help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue="" /> + help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue=""/> </inputs> <outputs> @@ -116,7 +124,7 @@ <tests> <test> - <!-- 3) Test all average with metadata --> + <!-- Test all average with metadata --> <param name="method" value="av_all"/> <param name="rdata_input" value="averageFragSpectra_output_all.RData"/> <param name="metadata_cond|metadata_select" value="true"/> @@ -127,6 +135,21 @@ <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/> </test> + <test> + <!-- Test custom adducts average with metadata --> + <param name="method" value="av_all"/> + <param name="rdata_input" value="averageFragSpectra_output_all.RData"/> + <param name="metadata_cond|metadata_select" value="true"/> + <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/> + <param name="xcms_group_cond|xcms_group_select" value="true"/> + <param name="xcms_group_cond|xcms_groupids" value="8,12"/> + <param name="metadata_cond|adduct_split" value="true"/> + <param name="include_adducts_custom" value="[M+]+,[M-H]-,[M+TEST SPACE+]+"/> + <output name="createMSP_output" file="createMSP_output_av_all_metadata_custom_adducts.msp"/> + </test> + + + </tests> <help><![CDATA[ ------------------------------
--- a/macros.xml Wed Apr 01 11:07:26 2020 -0400 +++ b/macros.xml Thu Apr 09 14:18:48 2020 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.12.2</token> - <token name="@GALAXY_TOOL_VERSION@">0</token> + <token name="@GALAXY_TOOL_VERSION@">1</token> <xml name="requirements"> <requirements> @@ -16,6 +16,9 @@ </requirements> </xml> + <xml name="text-adduct-regex-validator"> + <validator type="regex" message="Value may include alphanumeric characters, white space, commas, +, -, [ or ] ">[A-Za-z0-9,\[\] \+\-]+</validator> + </xml> <xml name="offsets"> <param argument="--minoffset" type="float" label="minoffset" value="0.5"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_output_av_all_metadata_custom_adducts.msp Thu Apr 09 14:18:48 2020 -0400 @@ -0,0 +1,108 @@ +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+NH4]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +isotope [4][M]+ +MS$FOCUSED_ION: PRECURSOR_TYPE [M+NH4]+ +AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N +CH$LINK: PUBCHEM CID:5328 +CH$NAME Unknown +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 + +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+H+NH3]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +isotope [4][M]+ +MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+ +AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N +CH$LINK: PUBCHEM CID:5328 +CH$NAME Unknown +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 + +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +isotope [4][M]+ +MS$FOCUSED_ION: PRECURSOR_TYPE [M+]+ +AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N +CH$LINK: PUBCHEM CID:5328 +CH$NAME Unknown +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 + +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M-H]- +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +isotope [4][M]+ +MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]- +AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N +CH$LINK: PUBCHEM CID:5328 +CH$NAME Unknown +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 + +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+TEST +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +isotope [4][M]+ +MS$FOCUSED_ION: PRECURSOR_TYPE [M+TEST +AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N +CH$LINK: PUBCHEM CID:5328 +CH$NAME Unknown +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 + +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:SPACE+]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +isotope [4][M]+ +MS$FOCUSED_ION: PRECURSOR_TYPE SPACE+]+ +AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N +CH$LINK: PUBCHEM CID:5328 +CH$NAME Unknown +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 +