| Previous changeset 3:1cba235b1972 (2020-04-09) Next changeset 5:84b2151fd8f4 (2020-11-13) |
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Commit message:
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950" |
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modified:
README.rst createDatabase.R macros.xml spectralMatching.R |
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| diff -r 1cba235b1972 -r 7856fc53df1d README.rst --- a/README.rst Thu Apr 09 14:15:03 2020 -0400 +++ b/README.rst Mon Aug 10 08:29:49 2020 -0400 |
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| @@ -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 |
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| diff -r 1cba235b1972 -r 7856fc53df1d createDatabase.R --- a/createDatabase.R Thu Apr 09 14:15:03 2020 -0400 +++ b/createDatabase.R Mon Aug 10 08:29:49 2020 -0400 |
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| @@ -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'){ |
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| diff -r 1cba235b1972 -r 7856fc53df1d macros.xml --- a/macros.xml Thu Apr 09 14:15:03 2020 -0400 +++ b/macros.xml Mon Aug 10 08:29:49 2020 -0400 |
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| @@ -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> |
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| diff -r 1cba235b1972 -r 7856fc53df1d spectralMatching.R --- a/spectralMatching.R Thu Apr 09 14:15:03 2020 -0400 +++ b/spectralMatching.R Mon Aug 10 08:29:49 2020 -0400 |
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| @@ -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, |