Mercurial > repos > galaxyp > cardinal_preprocessing
diff preprocessing.xml @ 11:e86a8be551b9 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0c667acd7cc0d0ef6c4e979ca29372b8c0d92c23"
| author | galaxyp |
|---|---|
| date | Tue, 06 Oct 2020 08:12:49 +0000 |
| parents | 5abc3ab4792c |
| children | e0669b1854b1 |
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--- a/preprocessing.xml Sun Sep 27 11:10:30 2020 +0000 +++ b/preprocessing.xml Tue Oct 06 08:12:49 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0"> +<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1"> <description> mass spectrometry imaging preprocessing </description> @@ -336,10 +336,12 @@ #if str($processed_cond.processed_file) == "processed": - msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun) + msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun") #else - msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun) + ## continuous file cannot be binned from m/z to m/z, therefore first cut m/z range and then do mzbin: + msidata = msidata[mz(msidata) >= $method.methods_conditional.mz_range.min_mz & mz(msidata) <= $method.methods_conditional.mz_range.max_mz,] + msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun") #end if