Mercurial > repos > tomnl > mspurity_flagremove
changeset 13:2445754177bb draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4f88143938cc198436c2691443832c87e2c31cd0
| author | tomnl |
|---|---|
| date | Tue, 24 Sep 2019 07:52:30 -0400 |
| parents | 2c8b5a640a04 |
| children | 568e12663295 |
| files | combineAnnotations.R macros.xml |
| diffstat | 2 files changed, 39 insertions(+), 16 deletions(-) [+] |
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--- a/combineAnnotations.R Fri Sep 13 11:49:43 2019 -0400 +++ b/combineAnnotations.R Tue Sep 24 07:52:30 2019 -0400 @@ -67,7 +67,7 @@ source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } source_local("dbconfig.R") }else{ - compoundDbType = opt$compoundDbType + compoundDbType = compoundDbType compoundDbName = NA compoundDbHost = NA compoundDbPort = NA @@ -79,7 +79,7 @@ summary_output <- msPurity::combineAnnotations( sm_resultPth = sm_resultPth, - compoundDbPth = opt$compoundDbPth, + compoundDbPth = compoundDbPth, metfrag_resultPth = opt$metfrag_resultPth, sirius_csi_resultPth = opt$sirius_csi_resultPth, probmetab_resultPth = opt$probmetab_resultPth,
--- a/macros.xml Fri Sep 13 11:49:43 2019 -0400 +++ b/macros.xml Tue Sep 24 07:52:30 2019 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.11.4</token> - <token name="@GALAXY_TOOL_VERSION@">0.2.5</token> + <token name="@GALAXY_TOOL_VERSION@">0.2.6</token> <xml name="requirements"> <requirements> @@ -108,7 +108,7 @@ <conditional name="@QL_SHRT@_dbPth_con"> <param name="@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" > <option value="sqlite" selected="@USER@" >SQLite database of (LC)-MS/MS data</option> - <option value="local_config" selected="@USER@" >Locally configured MySQL or Postgres database</option> + <option value="local_config" selected="@USER@" >Locally configured SQLite, MySQL or PostgreSQL database</option> <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option> </param> <when value="sqlite"> @@ -248,36 +248,59 @@ <when value="true"> <param name="@QL_SHRT@_instrumentTypes" type="select" multiple="true" help="" > - <option value="APCI-ITFT">APCI-ITFT</option> - <option value="CE-ESI-TOF" selected="true">CE-ESI-TOF</option> + <option value="APCI-ITFT" selected="true" >APCI-ITFT</option> + <option value="APCI-ITTOF" selected="true" >APCI-ITTOF</option> + <option value="CE-ESI-TOF" selected="true" >CE-ESI-TOF</option> <option value="CI-B">CI-B</option> <option value="EI-B">EI-B</option> <option value="EI-EBEB">EI-EBEB</option> - <option value="ESI-ITFT" selected="true">ESI-ITFT</option> - <option value="ESI-ITTOF" selected="true">ESI-ITTOF</option> - <option value="ESI-QTOF" selected="true">ESI-QTOF</option> + <option value="ESI-ITFT" selected="true" >ESI-ITFT</option> + <option value="ESI-ITTOF" selected="true" >ESI-ITTOF</option> + <option value="ESI-QFT" selected="true" >ESI-QFT</option> + <option value="ESI-QTOF" selected="true" >ESI-QTOF</option> + <option value="ESI-TOF" selected="true" >ESI-TOF</option> <option value="FAB-B">FAB-B</option> - <option value="FAB-BE-MS">FAB-BE-MS</option> + <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="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> <option value="GC-EI-QQ">GC-EI-QQ</option> <option value="GC-EI-TOF">GC-EI-TOF</option> - <option value="LC-APCI-QTOF">LC-APCI-QTOF</option> + <option value="GC-MS">GC-MS</option> + <option value="Hybrid FT">Hybrid FT</option> + <option value="in source CID" selected="true" >in source CID</option> + <option value="In-silico QTOF" selected="true" >In-silico QTOF</option> + <option value="Ion trap" selected="true" >Ion trap</option> + <option value="LC-APCI-ITFT" selected="true" >LC-APCI-ITFT</option> + <option value="LC-APCI-QTOF" selected="true" >LC-APCI-QTOF</option> + <option value="LC-APCI-Q" selected="true">LC-APCI-Q</option> <option value="LC-APPI-QQ">LC-APPI-QQ</option> <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option> <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option> <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option> - <option value="LC-ESI-Q">LC-ESI-Q</option> - <option value="LC-ESI-QFT" selected="true" >LC-ESI-QFT</option> + <option value="LC-ESI-Q" selected="true">LC-ESI-Q</option> + <option value="LC-ESI-QFT" selected="true">LC-ESI-QFT</option> <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option> <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option> <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option> <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option> - <option value="MALDI-QIT">MALDI-QIT</option> - <option value="MALDI-TOF">MALDI-TOF</option> - <option value="ALDI-TOFTOF">ALDI-TOFTOF</option> + <option value="LC-Q-TOF/MS" selected="true">LC-Q-TOF/MS</option> + <option value="LC-QTOF" selected="true">LC-QTOF</option> + <option value="Linear Ion Trap" selected="true">Linear Ion Trap</option> + <option value="LIT" selected="true">LIT</option> + <option value="MALDI-QIT" selected="true">MALDI-QIT</option> + <option value="MALDI-TOF" selected="true">MALDI-TOF</option> + <option value="MALDI-TOFTOF" selected="true">MALDI-TOFTOF</option> + <option value="orbitrap" selected="true">orbitrap</option> + <option value="QIT" selected="true">QIT</option> + <option value="QIT-FT" selected="true">QIT-FT</option> + <option value="QIT-TOF" selected="true">QIT-TOF</option> + <option value="QqQ" selected="true">QqQ</option> + <option value="Q-TOF" selected="true">Q-TOF</option> + <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option> <option value="none">None</option> </param> <param name="@QL_SHRT@_instrumentTypesUser" type="text" value=""