# HG changeset patch # User galaxyp # Date 1601971969 0 # Node ID e86a8be551b9ede2c7d3813e6f8777952262b8e6 # Parent 5abc3ab4792c0676fadae4c3dbfd61647ea1bada "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0c667acd7cc0d0ef6c4e979ca29372b8c0d92c23" diff -r 5abc3ab4792c -r e86a8be551b9 preprocessing.xml --- 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 @@ - + mass spectrometry imaging preprocessing @@ -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 diff -r 5abc3ab4792c -r e86a8be551b9 test-data/QC_analyze75.pdf Binary file test-data/QC_analyze75.pdf has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/QC_empty_spectra.pdf Binary file test-data/QC_empty_spectra.pdf has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/QC_imzml.pdf Binary file test-data/QC_imzml.pdf has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/QC_rdata.pdf Binary file test-data/QC_rdata.pdf has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results1.ibd Binary file test-data/preprocessing_results1.ibd has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results1.imzml Tue Oct 06 08:12:49 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results1.imzml.txt Tue Oct 06 08:12:49 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 216 Mai 10 17:37 ibd --rw-r--r-- 1 meli meli 18090 Mai 10 17:37 imzml +-rw-rw-r-- 1 meli meli 216 Oct 5 19:57 ibd +-rw-rw-r-- 1 meli meli 18090 Oct 5 19:57 imzml diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results1.pdf Binary file test-data/preprocessing_results1.pdf has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results2.ibd Binary file test-data/preprocessing_results2.ibd has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results2.imzml Tue Oct 06 08:12:49 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results2.imzml.txt Tue Oct 06 08:12:49 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 64 --rw-r--r-- 1 meli meli 37404 Mai 10 17:38 ibd --rw-r--r-- 1 meli meli 22796 Mai 10 17:38 imzml +-rw-rw-r-- 1 meli meli 37404 Oct 5 19:57 ibd +-rw-rw-r-- 1 meli meli 22796 Oct 5 19:57 imzml diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results2.pdf Binary file test-data/preprocessing_results2.pdf has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results3.ibd Binary file test-data/preprocessing_results3.ibd has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results3.imzml Tue Oct 06 08:12:49 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results3.imzml.txt Tue Oct 06 08:12:49 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 960 Mai 10 17:39 ibd --rw-r--r-- 1 meli meli 18112 Mai 10 17:39 imzml +-rw-rw-r-- 1 meli meli 960 Oct 5 19:58 ibd +-rw-rw-r-- 1 meli meli 18112 Oct 5 19:58 imzml diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results3.pdf Binary file test-data/preprocessing_results3.pdf has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results4.ibd Binary file test-data/preprocessing_results4.ibd has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results4.imzml Tue Oct 06 08:12:49 2020 +0000 @@ -9,8 +9,8 @@ - - + + diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results4.imzml.txt --- a/test-data/preprocessing_results4.imzml.txt Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results4.imzml.txt Tue Oct 06 08:12:49 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 84 --rw-rw-r-- 1 meli meli 62696 Sep 20 11:48 ibd --rw-rw-r-- 1 meli meli 18199 Sep 20 11:48 imzml +-rw-rw-r-- 1 meli meli 62696 Oct 5 19:58 ibd +-rw-rw-r-- 1 meli meli 18199 Oct 5 19:58 imzml diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results4.pdf Binary file test-data/preprocessing_results4.pdf has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results5.ibd Binary file test-data/preprocessing_results5.ibd has changed diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results5.imzml --- a/test-data/preprocessing_results5.imzml Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results5.imzml Tue Oct 06 08:12:49 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results5.imzml.txt --- a/test-data/preprocessing_results5.imzml.txt Sun Sep 27 11:10:30 2020 +0000 +++ b/test-data/preprocessing_results5.imzml.txt Tue Oct 06 08:12:49 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 428 --rw-r--r-- 1 meli meli 415936 Mai 10 17:40 ibd --rw-r--r-- 1 meli meli 18569 Mai 10 17:40 imzml +-rw-rw-r-- 1 meli meli 415936 Oct 5 19:59 ibd +-rw-rw-r-- 1 meli meli 18569 Oct 5 19:59 imzml diff -r 5abc3ab4792c -r e86a8be551b9 test-data/preprocessing_results5.pdf Binary file test-data/preprocessing_results5.pdf has changed