Mercurial > repos > eschen42 > w4mcorcov
comparison w4mcorcov_wrapper.R @ 5:50f60f94c034 draft
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
| author | eschen42 |
|---|---|
| date | Fri, 30 Mar 2018 14:59:19 -0400 |
| parents | e03582f26617 |
| children | 7bd523ca1f9a |
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| 4:8bba31f628da | 5:50f60f94c034 |
|---|---|
| 61 my_env$sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) | 61 my_env$sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) |
| 62 my_env$variableMetadata_in <- as.character(argVc["variableMetadata_in"]) | 62 my_env$variableMetadata_in <- as.character(argVc["variableMetadata_in"]) |
| 63 my_env$contrast_detail <- as.character(argVc["contrast_detail"]) | 63 my_env$contrast_detail <- as.character(argVc["contrast_detail"]) |
| 64 my_env$contrast_corcov <- as.character(argVc["contrast_corcov"]) | 64 my_env$contrast_corcov <- as.character(argVc["contrast_corcov"]) |
| 65 my_env$contrast_salience <- as.character(argVc["contrast_salience"]) | 65 my_env$contrast_salience <- as.character(argVc["contrast_salience"]) |
| 66 # print(sprintf("contrast_salience: %s", my_env$contrast_salience)) | |
| 67 | 66 |
| 68 # other parameters | 67 # other parameters |
| 69 | 68 |
| 70 my_env$tesC <- as.character(argVc["tesC"]) | 69 my_env$tesC <- as.character(argVc["tesC"]) |
| 71 my_env$facC <- as.character(argVc["facC"]) | 70 my_env$facC <- as.character(argVc["facC"]) |
| 72 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) | 71 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) |
| 73 my_env$levCSV <- as.character(argVc["levCSV"]) | 72 my_env$levCSV <- as.character(argVc["levCSV"]) |
| 74 my_env$matchingC <- as.character(argVc["matchingC"]) | 73 my_env$matchingC <- as.character(argVc["matchingC"]) |
| 75 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' | 74 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' |
| 76 my_env$labelOrthoFeatures <- as.logical(argVc["labelOrthoFeatures"]) | |
| 77 | 75 |
| 78 label_features <- my_env$labelFeatures | 76 label_features <- my_env$labelFeatures |
| 79 labelfeatures_check <- TRUE | 77 labelfeatures_check <- TRUE |
| 80 if ( is.na(label_features) ) { | 78 if ( is.na(label_features) ) { |
| 81 labelfeatures_check <- FALSE | 79 labelfeatures_check <- FALSE |
| 89 } | 87 } |
| 90 if ( !labelfeatures_check ) { | 88 if ( !labelfeatures_check ) { |
| 91 my_log("invalid argument: labelFeatures") | 89 my_log("invalid argument: labelFeatures") |
| 92 print(label_features) | 90 print(label_features) |
| 93 quit(save = "no", status = 10, runLast = TRUE) | 91 quit(save = "no", status = 10, runLast = TRUE) |
| 94 } | |
| 95 | |
| 96 tsv_action_factory <- function(file, colnames, append) { | |
| 97 return ( | |
| 98 function(tsv) { | |
| 99 write.table( | |
| 100 x = tsv | |
| 101 , file = file | |
| 102 , sep = "\t" | |
| 103 , quote = FALSE | |
| 104 , row.names = FALSE | |
| 105 , col.names = colnames | |
| 106 , append = append | |
| 107 ) | |
| 108 } | |
| 109 ) | |
| 110 } | 92 } |
| 111 | 93 |
| 112 corcov_tsv_colnames <- TRUE | 94 corcov_tsv_colnames <- TRUE |
| 113 corcov_tsv_append <- FALSE | 95 corcov_tsv_append <- FALSE |
| 114 corcov_tsv_action <- function(tsv) { | 96 corcov_tsv_action <- function(tsv) { |