Mercurial > repos > computational-metabolomics > mspurity_spectralmatching
changeset 4:aee10d29e82c draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
| author | computational-metabolomics |
|---|---|
| date | Mon, 10 Aug 2020 08:39:40 -0400 |
| parents | 15e3df50be3c |
| children | 829af6fecd96 |
| files | README.rst createDatabase.R macros.xml spectralMatching.R spectralMatching.xml |
| diffstat | 5 files changed, 15 insertions(+), 5 deletions(-) [+] |
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--- a/README.rst Thu Apr 09 14:11:20 2020 -0400 +++ b/README.rst Mon Aug 10 08:39:40 2020 -0400 @@ -3,13 +3,13 @@ |Build Status (Travis)| |Git| |Bioconda| |License| -Version v1.12.2+galaxy1 +Version v1.12.2+galaxy2 ------ - msPurity - bioconductor-mspurity v1.12.2 - Galaxy tools - - v1 + - v2 About ------ @@ -55,6 +55,11 @@ Changes ------------------------- +v1.12.2-galaxy2 + - Bug fix for using custom library sqlite database from Galaxy UI + - Bug fix for "allfrag" for createDatabase + + v1.12.2-galaxy1 - grpPeaklist reference incorrect in createDatabase.xml - Add custom adduct handling for createMSP
--- a/createDatabase.R Thu Apr 09 14:11:20 2020 -0400 +++ b/createDatabase.R Mon Aug 10 08:39:40 2020 -0400 @@ -94,7 +94,11 @@ print(pa@fileList) - +# Missing list element causes failures (should be updated +# in msPurity R package for future releases) +if (!exists('allfrag', where=pa@filter_frag_params)){ + pa@filter_frag_params$allfrag <- FALSE +} if (opt$xcms_camera_option=='xcms'){
--- a/macros.xml Thu Apr 09 14:11:20 2020 -0400 +++ b/macros.xml Mon Aug 10 08:39:40 2020 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.12.2</token> - <token name="@GALAXY_TOOL_VERSION@">1</token> + <token name="@GALAXY_TOOL_VERSION@">2</token> <xml name="requirements"> <requirements>
--- a/spectralMatching.R Thu Apr 09 14:11:20 2020 -0400 +++ b/spectralMatching.R Mon Aug 10 08:39:40 2020 -0400 @@ -292,6 +292,7 @@ q_check <- checkSPeakMeta(opt$q_dbPth, 'query') l_check <- checkSPeakMeta(opt$l_dbPth, 'library') + if (q_check && l_check){ sm <- msPurity::spectralMatching( q_purity = opt$q_purity,
--- a/spectralMatching.xml Thu Apr 09 14:11:20 2020 -0400 +++ b/spectralMatching.xml Mon Aug 10 08:39:40 2020 -0400 @@ -19,7 +19,7 @@ #if $Library.l_dbPth_con.l_dbPth_select == 'msPurityData' --l_defaultDb - #else if $Library.l_dbPth_con.l_dbPth_select == 'userdb_sqlite' + #else if $Library.l_dbPth_con.l_dbPth_select == 'sqlite' --l_dbPth=$Library.l_dbPth_con.l_dbPth #end if