Mercurial > repos > eschen42 > w4mclassfilter

comparison w4mclassfilter_wrapper.R @ 6:f1eabb5973b1 draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 08a878ac05ac0c05eafac27b9ebaadb88ae21eb7
author eschen42
date Thu, 11 Jan 2018 20:22:14 -0500
parents ae791fe4fbe9
children 518cc205f289
comparison
equal deleted inserted replaced
5:ae791fe4fbe9 6:f1eabb5973b1
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