Mercurial > repos > eschen42 > w4mclassfilter
diff w4mclassfilter_wrapper.R @ 6:38ccf6722d54 draft
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
author | eschen42 |
---|---|
date | Mon, 15 Jan 2018 14:06:39 -0500 |
parents | 499c7ecfa834 |
children | d5cf23369d12 |
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--- a/w4mclassfilter_wrapper.R Thu Sep 07 17:41:09 2017 -0400 +++ b/w4mclassfilter_wrapper.R Mon Jan 15 14:06:39 2018 -0500 @@ -82,8 +82,8 @@ # other parameters +wildcards <- as.logical(argVc["wildcards"]) sampleclassNames <- as.character(argVc["sampleclassNames"]) -wildcards <- as.logical(argVc["wildcards"]) sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] if (wildcards) { sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) @@ -93,22 +93,26 @@ classnameColumn <- as.character(argVc["classnameColumn"]) samplenameColumn <- as.character(argVc["samplenameColumn"]) +variable_range_filter <- as.character(argVc["variable_range_filter"]) +variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] + ##------------------------------ ## Computation ##------------------------------ result <- w4m_filter_by_sample_class( - dataMatrix_in = dataMatrix_in -, sampleMetadata_in = sampleMetadata_in -, variableMetadata_in = variableMetadata_in -, dataMatrix_out = dataMatrix_out -, sampleMetadata_out = sampleMetadata_out -, variableMetadata_out = variableMetadata_out -, classes = sampleclassNames -, include = inclusive -, class_column = classnameColumn -, samplename_column = samplenameColumn -, failure_action = my_print + dataMatrix_in = dataMatrix_in +, sampleMetadata_in = sampleMetadata_in +, variableMetadata_in = variableMetadata_in +, dataMatrix_out = dataMatrix_out +, sampleMetadata_out = sampleMetadata_out +, variableMetadata_out = variableMetadata_out +, classes = sampleclassNames +, include = inclusive +, class_column = classnameColumn +, samplename_column = samplenameColumn +, variable_range_filter = variable_range_filter +, failure_action = my_print ) my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",