Mercurial > repos > eschen42 > w4mclassfilter
comparison w4mclassfilter_wrapper.R @ 6:38ccf6722d54 draft
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
author | eschen42 |
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date | Mon, 15 Jan 2018 14:06:39 -0500 |
parents | 499c7ecfa834 |
children | d5cf23369d12 |
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5:2cdf7d5982c8 | 6:38ccf6722d54 |
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80 variableMetadata_in <- as.character(argVc["variableMetadata_in"]) | 80 variableMetadata_in <- as.character(argVc["variableMetadata_in"]) |
81 variableMetadata_out <- as.character(argVc["variableMetadata_out"]) | 81 variableMetadata_out <- as.character(argVc["variableMetadata_out"]) |
82 | 82 |
83 # other parameters | 83 # other parameters |
84 | 84 |
85 wildcards <- as.logical(argVc["wildcards"]) | |
85 sampleclassNames <- as.character(argVc["sampleclassNames"]) | 86 sampleclassNames <- as.character(argVc["sampleclassNames"]) |
86 wildcards <- as.logical(argVc["wildcards"]) | |
87 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] | 87 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] |
88 if (wildcards) { | 88 if (wildcards) { |
89 sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) | 89 sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) |
90 sampleclassNames <- utils::glob2rx(sampleclassNames, trim.tail = FALSE) | 90 sampleclassNames <- utils::glob2rx(sampleclassNames, trim.tail = FALSE) |
91 } | 91 } |
92 inclusive <- as.logical(argVc["inclusive"]) | 92 inclusive <- as.logical(argVc["inclusive"]) |
93 classnameColumn <- as.character(argVc["classnameColumn"]) | 93 classnameColumn <- as.character(argVc["classnameColumn"]) |
94 samplenameColumn <- as.character(argVc["samplenameColumn"]) | 94 samplenameColumn <- as.character(argVc["samplenameColumn"]) |
95 | 95 |
96 variable_range_filter <- as.character(argVc["variable_range_filter"]) | |
97 variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] | |
98 | |
96 ##------------------------------ | 99 ##------------------------------ |
97 ## Computation | 100 ## Computation |
98 ##------------------------------ | 101 ##------------------------------ |
99 | 102 |
100 result <- w4m_filter_by_sample_class( | 103 result <- w4m_filter_by_sample_class( |
101 dataMatrix_in = dataMatrix_in | 104 dataMatrix_in = dataMatrix_in |
102 , sampleMetadata_in = sampleMetadata_in | 105 , sampleMetadata_in = sampleMetadata_in |
103 , variableMetadata_in = variableMetadata_in | 106 , variableMetadata_in = variableMetadata_in |
104 , dataMatrix_out = dataMatrix_out | 107 , dataMatrix_out = dataMatrix_out |
105 , sampleMetadata_out = sampleMetadata_out | 108 , sampleMetadata_out = sampleMetadata_out |
106 , variableMetadata_out = variableMetadata_out | 109 , variableMetadata_out = variableMetadata_out |
107 , classes = sampleclassNames | 110 , classes = sampleclassNames |
108 , include = inclusive | 111 , include = inclusive |
109 , class_column = classnameColumn | 112 , class_column = classnameColumn |
110 , samplename_column = samplenameColumn | 113 , samplename_column = samplenameColumn |
111 , failure_action = my_print | 114 , variable_range_filter = variable_range_filter |
115 , failure_action = my_print | |
112 ) | 116 ) |
113 | 117 |
114 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", | 118 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", |
115 as.character(result), "\n", sep = "") | 119 as.character(result), "\n", sep = "") |
116 | 120 |