Mercurial > repos > galaxyp > cardinal_data_exporter

comparison data_exporter.xml @ 3:d94770c22f13 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
author galaxyp
date Thu, 28 Feb 2019 09:24:07 -0500
parents e30d8b72415f
children e521b5767819
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2:e30d8b72415f 3:d94770c22f13
222 222
223 #end if 223 #end if
224 #if str($tabular_annotation.load_annotation) == 'yes_annotation': 224 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
225 225
226 colnames(annotation_input) = c("x_values", "y_values", "annotation") 226 colnames(annotation_input) = c("x_values", "y_values", "annotation")
227 spectra_df = merge(annotation_input,spectra_df, by=c("x_values", "y_values")) 227 spectra_df = merge(spectra_df,annotation_input, by=c("x_values", "y_values"), all.x=TRUE)
228 228
229 ## sort columns to have spectra_names as rowname in first column 229 ## sort columns to have spectra_names as rowname in first column
230 #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants": 230 #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":
231 spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "m/z count", "annotation")] 231 spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "m/z count", "annotation")]
232 #else 232 #else