Mercurial > repos > computational-metabolomics > mspurity_dimspredictpuritysingle
changeset 7:2ce66d2f6a24 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
| author | computational-metabolomics |
|---|---|
| date | Tue, 08 Feb 2022 13:59:55 +0000 |
| parents | 090775983be7 |
| children | 75b761fbacc0 |
| files | README.rst dimsPredictPuritySingle.xml filterFragSpectra.R macros.xml |
| diffstat | 4 files changed, 21 insertions(+), 12 deletions(-) [+] |
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--- a/README.rst Thu Mar 04 12:24:27 2021 +0000 +++ b/README.rst Tue Feb 08 13:59:55 2022 +0000 @@ -3,13 +3,13 @@ |Build Status (Travis)| |Git| |Bioconda| |License| -Version v1.16.2+galaxy0 +Version v1.16.2+galaxy1 ------------------------ - msPurity - bioconductor-mspurity v1.16.2 - Galaxy tools - - v0 + - v1 About ------ @@ -32,8 +32,6 @@ * Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity - - Dependencies ------------------ Dependencies for these Galaxy tools should be handled by CONDA. @@ -53,8 +51,13 @@ - 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 ------------------------- +v1.16.2-galaxy1 + - Fix for "scan" option for spectral matching + - Add allfrag option for filterFragSpectra + v1.16.2-galaxy0 - Version bump - Fix for intra spectral matching
--- a/dimsPredictPuritySingle.xml Thu Mar 04 12:24:27 2021 +0000 +++ b/dimsPredictPuritySingle.xml Tue Feb 08 13:59:55 2022 +0000 @@ -63,13 +63,11 @@ </param> <when value="mzML_file"> <param argument="--mzML_file" name="source" type="data" format="mzml" label="Single *.mzML" > - <validator type="empty_field" /> </param> </when> <when value="mzML_data_collection"> <param argument="--mzML_files" name="source" type="data_collection" label="Data collection containing *.mzml files" > - <validator type="empty_field" /> </param> <param argument="--mzML_filename" type="text" label="Name of file to to calculate purity from" help=""/> </when> @@ -78,7 +76,6 @@ <param argument="--mzML_file" name="source" type="text" size="40" label="Library directory containing *.mzml files (dimspy input only) or path to an individual .mzML file"> - <validator type="empty_field" /> </param> </when>
--- a/filterFragSpectra.R Thu Mar 04 12:24:27 2021 +0000 +++ b/filterFragSpectra.R Tue Feb 08 13:59:55 2022 +0000 @@ -17,7 +17,8 @@ make_option("--snr", default = 0.0), make_option("--rmp", action = "store_true"), - make_option("--snmeth", default = "median", type = "character") + make_option("--snmeth", default = "median", type = "character"), + make_option("--allfrag", action = "store_true") ) opt <- parse_args(OptionParser(option_list = option_list)) @@ -39,12 +40,19 @@ opt$rmp <- TRUE } +if (is.null(opt$allfrag)) { + opt$allfrag <- FALSE +}else{ + opt$allfrag <- TRUE +} + pa <- filterFragSpectra(pa, ilim = opt$ilim, plim = opt$plim, ra = opt$ra, snr = opt$snr, rmp = opt$rmp, + allfrag = opt$allfrag, snmeth = opt$snmeth) print(pa)
--- a/macros.xml Thu Mar 04 12:24:27 2021 +0000 +++ b/macros.xml Tue Feb 08 13:59:55 2022 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.16.2</token> - <token name="@GALAXY_TOOL_VERSION@">0</token> + <token name="@GALAXY_TOOL_VERSION@">1</token> <xml name="requirements"> <requirements> @@ -271,7 +271,7 @@ <option value="FAB-BE">FAB-BE</option> <option value="FAB-EB">FAB-EB</option> <option value="FAB-EBEB">FAB-EBEB</option> - <option value="FAB-EBEB">FD-B</option> + <option value="FD-B">FD-B</option> <option value="FI-B">FI-B</option> <option value="Flow-injection QqQ/MS">Flow-injection QqQ/MS</option> <option value="GC-EI-Q">GC-EI-Q</option> @@ -333,13 +333,14 @@ <conditional name="@QL_SHRT@_spectraTypes_cond"> <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?" - help="" /> + help="Note that when using 'scan' spectra types the spectraFilter option may need to be FALSE + if 'allfrag' was not selecting when performing filterFragSpectra or if no filtering was performed at all" /> <when value="true"> <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" > <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option> <option value="inter">Averaged inter spectra</option> <option value="intra">Averaged intra spectra </option> - <option value="scans">All individual scans</option> + <option value="scan">All individual scans (may need to set spectraFilter to false with this option)</option> <option value="NA">Not applicable/defined</option> </param> </when>