removing srcdir

131fc2b4 · Konrad Zych · 9802edad · 131fc2b4 · 131fc2b4 · 131fc2b4
Commit 131fc2b4 authored Jan 11, 2018 by Konrad Zych
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,18 +13,18 @@ test:
  stage: test
  script:
    - Rscript 00_setup.r
-    - Rscript 01_validate_data.r --srcdir .. --metadata_in num_metadata_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --metadata_out valMetaData.tsv --label_in label_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --label_out valLabel.tsv --feat_in feat_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --feat_out valFeat.tsv
-    - Rscript 02_select_samples.r --srcdir .. --metadata_in valMetaData.tsv --metadata_out valMetaData_sel.tsv --label_in valLabel.tsv --label_out valLabel_sel.tsv --feat_in valFeat.tsv --feat_out valFeat_sel.tsv --filter_var="age" --allowed_range="[0,120]"
-    - Rscript 03_check_for_confounders.r --srcdir .. --metadata_in valMetaData_sel.tsv --plot metaCheck.pdf --label_in valLabel_sel.tsv
+    - Rscript 01_validate_data.r --metadata_in num_metadata_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --metadata_out valMetaData.tsv --label_in label_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --label_out valLabel.tsv --feat_in feat_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --feat_out valFeat.tsv
+    - Rscript 02_select_samples.r --metadata_in valMetaData.tsv --metadata_out valMetaData_sel.tsv --label_in valLabel.tsv --label_out valLabel_sel.tsv --feat_in valFeat.tsv --feat_out valFeat_sel.tsv --filter_var="age" --allowed_range="[0,120]"
+    - Rscript 03_check_for_confounders.r --metadata_in valMetaData_sel.tsv --plot metaCheck.pdf --label_in valLabel_sel.tsv
    - Rscript 04_filter_features.r --feat_in valFeat_sel.tsv --feat_out valFeat_sel_filtered.tsv --method="abundance" --cutoff="0.001" --recomp_prop="FALSE" --rm_unmapped="TRUE"
-    - Rscript 05_check_associations.r --srcdir .. --feat_in valFeat_sel_filtered.tsv --label_in valLabel_sel.tsv --plot assoc.pdf --col_scheme="RdYlBu" --alpha="0.7" --min_fc="0" --mult_test="fdr" --max_show="50" --detect_limit="1e-06" --plot_type="bean"
+    - Rscript 05_check_associations.r --feat_in valFeat_sel_filtered.tsv --label_in valLabel_sel.tsv --plot assoc.pdf --col_scheme="RdYlBu" --alpha="0.7" --min_fc="0" --mult_test="fdr" --max_show="50" --detect_limit="1e-06" --plot_type="bean"
    - Rscript 06_normalize_features.r --feat_in valFeat_sel_filtered.tsv --feat_out valFeat_sel_norm.tsv --param_out param_out.tsv --method="log.unit" --log_n0="1e-08" --sd_min_quantile="0.2" --vector_norm="2" --norm_margin="1"
    - Rscript 07_add_metadata_as_predictor.r --feat_in valFeat_sel_norm.tsv --feat_out valFeat_sel_norm.tsv --metadata_in valMetaData_sel.tsv --pred_names="fobt" --std_meta="TRUE"
-    - Rscript 08_split_data.r --srcdir .. --label_in valLabel_sel.tsv --train_sets trainSets.tsv --test_sets testSets.tsv --num_folds="10" --resample="5" --stratify="TRUE" --inseparable="NULL" --metadata_in valMetaData_sel.tsv
-    - Rscript 09_train_models.r --srcdir .. --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --train_sets trainSets.tsv --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2"
-    - Rscript 10_make_predictions.r --srcdir .. --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --test_sets testSets.tsv --pred pred.tsv --mlr_models_list models.RData
-    - Rscript 11_evaluate_predictions.r --srcdir .. --label_in valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
-    - Rscript 12_interpret_model.r --srcdir .. --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --metadata_in valMetaData_sel.tsv --mlr_models_list models.RData --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
+    - Rscript 08_split_data.r --label_in valLabel_sel.tsv --train_sets trainSets.tsv --test_sets testSets.tsv --num_folds="10" --resample="5" --stratify="TRUE" --inseparable="NULL" --metadata_in valMetaData_sel.tsv
+    - Rscript 09_train_models.r --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --train_sets trainSets.tsv --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2"
+    - Rscript 10_make_predictions.r --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --test_sets testSets.tsv --pred pred.tsv --mlr_models_list models.RData
+    - Rscript 11_evaluate_predictions.r --label_in valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
+    - Rscript 12_interpret_model.r --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --metadata_in valMetaData_sel.tsv --mlr_models_list models.RData --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
  only:
    - master
    - development

--- a/NAMESPACE
+++ b/NAMESPACE
 # Generated by roxygen2: do not edit by hand

 export(add.meta.pred)
-export(appendDirName)
 export(assign.fold)
 export(check.associations)
 export(confounder.check)

--- a/R/io_utils.r
+++ b/R/io_utils.r
@@ -131,17 +131,6 @@ read.meta <- function(fn.in.meta){
  invisible(meta)
 }

-#' @title Append source directory path
-#' @description Append / at the end of the name of the directory path if it is not there
-#' @param source.dir string with path to the source directory
-#' @export
-#' @return string with / at the end
-appendDirName <- function(source.dir){
-  if (substr(source.dir, nchar(source.dir), nchar(source.dir)) != '/') {
-    source.dir <- paste(source.dir, '/', sep='')
-  }
-  invisible(source.dir)
-}

 ##### auxiliary function to trim whitespace from string
 # returns string without leading or trailing whitespace

--- a/Rscript_flavor/01_validate_data.r
+++ b/Rscript_flavor/01_validate_data.r
@@ -17,7 +17,6 @@ suppressMessages(library('SIAMCAT'))

 # define arguments
 option_list <- list(
-  make_option(c('-s', '--srcdir'),  type='character', help='Source directory of this and other utility scripts'),
  make_option('--metadata_in',      type='character', help='Input file containing meta-data'),
  make_option('--metadata_out',     type='character', default = "meta_validated.tsv",
                                    help='Output file to which validated meta-data is written'),
@@ -35,7 +34,6 @@ opt          <- parse_args(OptionParser(option_list=option_list))
 # print parameters of the run
 cat("=== 01_data_validator.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('srcdir       =', opt$srcdir, '\n')
 cat('metadata_in  =', opt$metadata_in, '\n')
 cat('metadata_out =', opt$metadata_out, '\n')
 cat('label_in     =', opt$label_in, '\n')
@@ -44,7 +42,6 @@ cat('feat_in      =', opt$feat_in, '\n')
 cat('feat_out     =', opt$feat_out, '\n')
 cat('\n')

-source.dir <- appendDirName(opt$srcdir)
 start.time <- proc.time()[1]

 # reading in the files

--- a/Rscript_flavor/02_select_samples.r
+++ b/Rscript_flavor/02_select_samples.r
@@ -17,7 +17,6 @@ suppressMessages(library('optparse'))
 suppressMessages(library('SIAMCAT'))
 # define arguments
 option_list <- list(
-    make_option(c('-s', '--srcdir'), type='character',               help='Source directory of this and other utility scripts'),
    make_option('--metadata_in',     type='character',               help='Input file containing meta-data'),
    make_option('--metadata_out',    type='character',               help='Output file to which meta-data after selection is written'),
    make_option('--label_in',        type='character',               help='Input file containing labels'),
@@ -33,7 +32,6 @@ opt           <- parse_args(OptionParser(option_list=option_list))
 # print parameters of the run
 cat("=== 02_sample_selector.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('srcdir        =', opt$srcdir, '\n')
 cat('metadata_in   =', opt$metadata_in, '\n')
 cat('metadata_out  =', opt$metadata_out, '\n')
 cat('label_in      =', opt$label_in, '\n')
@@ -44,7 +42,6 @@ cat('filter_var    =', opt$filter_var, '\n')
 cat('allowed_range =', opt$allowed_range, '\n')
 cat('allowed_set   =', opt$allowed_set, '\n')

-source.dir  <- appendDirName(opt$srcdir)
 start.time  <- proc.time()[1]



--- a/Rscript_flavor/03_check_for_confounders.r
+++ b/Rscript_flavor/03_check_for_confounders.r
@@ -17,7 +17,6 @@ suppressMessages(library('SIAMCAT'))

 # define arguments
 option_list    <- list(
-  make_option(c('-s', '--srcdir'), type='character', help='Source directory of this and other utility scripts'),
  make_option('--metadata_in',     type='character', help='Input file containing meta-data'),
  make_option('--label_in',        type='character', help='Input file containing labels'),
  make_option('--plot',            type='character', help='Output pdf file which will contain resulting plots')
@@ -28,13 +27,11 @@ opt          <- parse_args(OptionParser(option_list=option_list))
 # print parameters of the run
 cat("=== 03_confounder_check.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('source.dir   =', opt$srcdir, '\n')
 cat('metadata_in  =', opt$metadata_in, '\n')
 cat('label_in     =', opt$label_in, '\n')
 cat('plot         =', opt$plot, '\n')
 cat('\n')

-source.dir   <- appendDirName(opt$srcdir)
 start.time   <- proc.time()[1]



--- a/Rscript_flavor/05_check_associations.r
+++ b/Rscript_flavor/05_check_associations.r
@@ -17,7 +17,6 @@ suppressMessages(library('SIAMCAT'))

 # define arguments
 option_list <- list(
-  make_option(c('-s', '--srcdir'), type='character',                   help='Source directory of this and other utility scripts'),
  make_option('--label_in',        type='character',                   help='Input file containing labels'),
  make_option('--feat_in',         type='character',                   help='Input file containing features'),
  make_option('--plot',            type='character',                   help='Output pdf file which will contain resulting plots'),
@@ -35,7 +34,6 @@ option_list <- list(
 opt          <- parse_args(OptionParser(option_list=option_list))
 cat("=== 05_association_check.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('srcdir       =', opt$srcdir, '\n')
 cat('label_in     =', opt$label_in, '\n')
 cat('feat_in      =', opt$feat_in, '\n')
 cat('plot         =', opt$plot, '\n')
@@ -50,7 +48,6 @@ cat('plot_type    =', opt$plot_type, '\n')
 cat('\n')

 ### If variable source.dir does not end with "/", append "/" to end of source.dir
-source.dir <- appendDirName(opt$srcdir)
 start.time <- proc.time()[1]

 feat  <- read.features(opt$feat_in)

--- a/Rscript_flavor/08_split_data.r
+++ b/Rscript_flavor/08_split_data.r
@@ -20,7 +20,6 @@ r.seed          <- 223311

 # define arguments
 option_list     <- list(
-  make_option(c('-s', '--srcdir'), type='character',                 help='Source directoyr of utility scripts'),
  make_option('--label_in',        type='character',                 help='Input file containing labels'),
  make_option('--train_sets',      type='character',                 help='Output file containing training sets'),
  make_option('--test_sets',       type='character',                 help='Output file containing test sets'),
@@ -39,7 +38,6 @@ opt            <- parse_args(OptionParser(option_list=option_list))
 # print parameters of the run
 cat("=== 08_data_splitter.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('source.dir  =', opt$srcdir, '\n')
 cat('label_in    =', opt$label_in, '\n')
 cat('train_sets  =', opt$train_sets, '\n')
 cat('test_sets   =', opt$test_sets, '\n')
@@ -50,7 +48,6 @@ cat('inseparable =', opt$inseparable, '\n')
 cat('metadata_in =', opt$metadata_in, '\n')
 cat('\n')

-source.dir  <- appendDirName(opt$srcdir)
 start.time  <- proc.time()[1]
 set.seed(r.seed)


--- a/Rscript_flavor/09_train_models.r
+++ b/Rscript_flavor/09_train_models.r
@@ -25,7 +25,6 @@ DEBUG.CHECKS <- FALSE                # performs additional checks (asserting tha

 # define arguments
 option_list <- list(
-    make_option(c('-s', '--srcdir'),   type='character',                  help='Source directory of this and other utility scripts'),
    make_option('--feat_in',           type='character',                  help='Input file containing features'),
    make_option('--label_in',          type='character',                  help='Input file containing labels'),
    make_option('--method',            type='character', default='lasso', help='class of learner, directly passed to mlr::makeLearner'),
@@ -47,7 +46,6 @@ DEBUG.CHECKS <- FALSE                # performs additional checks (asserting tha
 # print parameters of the run
 cat("=== 09_plm_trainer.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('srcdir            =', opt$srcdir,  '\n')
 cat('feat_in           =', opt$feat_in, '\n')
 cat('label_in          =', opt$label_in, '\n')
 cat('method            =', opt$method, '\n')
@@ -60,9 +58,6 @@ cat('param_set         =', opt$param_set, '\n')
 cat('\n')


-
-opt$srcdir <- appendDirName(opt$srcdir)
-
 # optional parameters will be reset to NULL if specified as 'NULL', 'NONE' or 'UNKNOWN'
 if (toupper(opt$train_sets)=='NULL' || toupper(opt$train_sets)=='NONE' || toupper(opt$train_sets)=='UNKNOWN') {
  opt$train_sets= NULL

--- a/Rscript_flavor/10_make_predictions.r
+++ b/Rscript_flavor/10_make_predictions.r
@@ -19,7 +19,6 @@ suppressMessages(library('methods'))

 # define arguments
  option_list = list(
-    make_option(c('-s', '--srcdir'), type='character',                     help='Source directory of this and other utility scripts'),
    make_option('--feat_in',         type='character',                     help='Input file containing features'),
    make_option('--mlr_models_list', type='character',                     help='Input RData file containing the trained models'),
    make_option('--label_in',        type='character', default='NULL',     help='Input file containing labels'),
@@ -31,7 +30,6 @@ opt            <- parse_args(OptionParser(option_list=option_list))
 # print parameters of the run
 cat("=== 10_plm_predictor.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('srcdir          =', opt$srcdir,        '\n')
 cat('feat_in         =', opt$feat_in,      '\n')
 cat('mlr_models_list =', opt$mlr_models_list,'\n')
 cat('label_in        =', opt$label_in,     '\n')
@@ -39,7 +37,6 @@ cat('test_sets       =', opt$test_sets,    '\n')
 cat('pred            =', opt$pred,           '\n')
 cat('\n')

-source.dir <- appendDirName(opt$srcdir)
 # optional parameters will be reset to NULL if specified as 'NULL', 'NONE' or 'UNKNOWN'
 if (is.null(opt$test_sets)) {
  opt$test_sets = NULL

--- a/Rscript_flavor/11_evaluate_predictions.r
+++ b/Rscript_flavor/11_evaluate_predictions.r
@@ -19,7 +19,6 @@ suppressMessages(library('SIAMCAT'))
 # define arguments
  option_list = list(
  #make_option('--pkgdir', type='character', help='Source directory of dataprep'),
-  make_option(c('-s', '--srcdir'),    type='character',                help='Source directory of this and other utility scripts'),
  make_option('--label_in',              type='character',                help='Input file containing labels'),
  make_option('--pred',               type='character',                help='Input file containing the trained classification model(s)'),
  make_option('--plot',               type='character',                help='Output file for plotting'),
@@ -31,7 +30,6 @@ suppressMessages(library('SIAMCAT'))
 opt            <- parse_args(OptionParser(option_list=option_list))
 cat("=== 11_model_evaler.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('srcdir             =', opt$srcdir, '\n')
 cat('label_in           =', opt$label_in, '\n')
 cat('pred               =', opt$pred, '\n')
 cat('plot               =', opt$plot, '\n')
@@ -40,7 +38,6 @@ cat('output_results     =', opt$output_results, '\n')
 cat('\n')

 ### If variable source.dir does not end with "/", append "/" to end of source.dir
-source.dir <- appendDirName(opt$srcdir)
 start.time <- proc.time()[1]
 label      <- read.labels(opt$label_in)


--- a/Rscript_flavor/12_interpret_model.r
+++ b/Rscript_flavor/12_interpret_model.r
@@ -18,7 +18,6 @@ suppressMessages(library('SIAMCAT'))

 # define arguments
 option_list  <-  list(
-  make_option(c('-s', '--srcdir'), type='character',                   help='Source directory of this and other utility scripts'),
  make_option('--label_in',        type='character',                   help='Input file containing labels'),
  make_option('--feat_in',         type='character',                   help='Input file containing features'),
  make_option('--origin_feat',     type='character',                   help='Input file containing unnormalized/filtered features'),
@@ -38,7 +37,6 @@ option_list  <-  list(
 opt            <- parse_args(OptionParser(option_list=option_list))
 cat("=== 12_model_interpretor.r\n")
 cat("=== Paramaters of the run:\n\n")
-cat('srcdir          =', opt$srcdir, '\n')
 cat('feat            =', opt$feat, '\n')
 cat('origin_feat.    =', opt$origin_feat, '\n')
 cat('metadata_in     =', opt$metadata_in, '\n')
@@ -51,12 +49,6 @@ cat('consens_thres   =', opt$consens_thres, '\n')
 cat('heatmap_type    =', opt$heatmap_type, '\n')
 cat('\n')

-### If variable source.dir does not end with "/", append "/" to end of source.dir
-source.dir <- appendDirName(opt$srcdir)
-# TODO (remove last check)
-# optional parameters will be reset to NULL if specified as 'NULL', 'NONE' or 'UNKNOWN'
-
-
 ### read features and labels
 start.time <- proc.time()[1]
 feat        <- read.features(opt$feat)

--- a/Rscript_flavor/execute.sh
+++ b/Rscript_flavor/execute.sh
 Rscript 00_setup.r
-Rscript 01_validate_data.r --srcdir .. --metadata_in num_metadata_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --metadata_out valMetaData.tsv --label_in label_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --label_out valLabel.tsv --feat_in feat_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --feat_out valFeat.tsv
-Rscript 02_select_samples.r --srcdir .. --metadata_in valMetaData.tsv --metadata_out valMetaData_sel.tsv --label_in valLabel.tsv --label_out valLabel_sel.tsv --feat_in valFeat.tsv --feat_out valFeat_sel.tsv --filter_var="age" --allowed_range="[0,120]"
-Rscript 03_check_for_confounders.r --srcdir .. --metadata_in valMetaData_sel.tsv --plot metaCheck.pdf --label_in valLabel_sel.tsv
+Rscript 01_validate_data.r --metadata_in num_metadata_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --metadata_out valMetaData.tsv --label_in label_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --label_out valLabel.tsv --feat_in feat_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --feat_out valFeat.tsv
+Rscript 02_select_samples.r --metadata_in valMetaData.tsv --metadata_out valMetaData_sel.tsv --label_in valLabel.tsv --label_out valLabel_sel.tsv --feat_in valFeat.tsv --feat_out valFeat_sel.tsv --filter_var="age" --allowed_range="[0,120]"
+Rscript 03_check_for_confounders.r --metadata_in valMetaData_sel.tsv --plot metaCheck.pdf --label_in valLabel_sel.tsv
 Rscript 04_filter_features.r --feat_in valFeat_sel.tsv --feat_out valFeat_sel_filtered.tsv --method="abundance" --cutoff="0.001" --recomp_prop="FALSE" --rm_unmapped="TRUE"
-Rscript 05_check_associations.r --srcdir .. --feat_in valFeat_sel_filtered.tsv --label_in valLabel_sel.tsv --plot assoc.pdf --col_scheme="RdYlBu" --alpha="0.7" --min_fc="0" --mult_test="fdr" --max_show="50" --detect_limit="1e-06" --plot_type="bean"
+Rscript 05_check_associations.r --feat_in valFeat_sel_filtered.tsv --label_in valLabel_sel.tsv --plot assoc.pdf --col_scheme="RdYlBu" --alpha="0.7" --min_fc="0" --mult_test="fdr" --max_show="50" --detect_limit="1e-06" --plot_type="bean"
 Rscript 06_normalize_features.r --feat_in valFeat_sel_filtered.tsv --feat_out valFeat_sel_norm.tsv --param_out param_out.tsv --method="log.unit" --log_n0="1e-08" --sd_min_quantile="0.2" --vector_norm="2" --norm_feature="FALSE" --norm_sample="TRUE" --norm_global="FALSE"
 Rscript 07_add_metadata_as_predictor.r --feat_in valFeat_sel_norm.tsv --feat_out valFeat_sel_norm.tsv --metadata_in valMetaData_sel.tsv --pred_names="fobt" --std_meta="TRUE" 
-Rscript 08_split_data.r --srcdir .. --label_in valLabel_sel.tsv --train_sets trainSets.tsv --test_sets testSets.tsv --num_folds="10" --resample="5" --stratify="TRUE" --inseparable="NULL" --metadata_in valMetaData_sel.tsv
-Rscript 09_train_models.r --srcdir .. --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --train_sets trainSets.tsv --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2" --model models.tsv --model_matrix model.matrix.txt
-Rscript 10_make_predictions.r --srcdir .. --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --test_sets testSets.tsv --pred pred.tsv --mlr_models_list models.RData --model_matrix model.matrix.txt --hyperpars hyperpars.txt
-Rscript 11_evaluate_predictions.r --srcdir .. --label valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
-Rscript 12_interpret_model.r --srcdir .. --label valLabel_sel.tsv --feat valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --meta valMetaData_sel.tsv --model models.tsv --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
\ No newline at end of file
+Rscript 08_split_data.r --label_in valLabel_sel.tsv --train_sets trainSets.tsv --test_sets testSets.tsv --num_folds="10" --resample="5" --stratify="TRUE" --inseparable="NULL" --metadata_in valMetaData_sel.tsv
+Rscript 09_train_models.r --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --train_sets trainSets.tsv --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2" --model models.tsv --model_matrix model.matrix.txt
+Rscript 10_make_predictions.r --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --test_sets testSets.tsv --pred pred.tsv --mlr_models_list models.RData --model_matrix model.matrix.txt --hyperpars hyperpars.txt
+Rscript 11_evaluate_predictions.r --label valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
+Rscript 12_interpret_model.r --label valLabel_sel.tsv --feat valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --meta valMetaData_sel.tsv --model models.tsv --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
\ No newline at end of file
--- a/docs/LICENSE.html
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--- a/docs/index.html
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