# HG changeset patch
# User mingchen0919
# Date 1521568744 14400
# Node ID f8ac93c417209612370cf2d069ce9f50b2cff4b3
# Parent a88f12177e6fdbcadf6764fdd642ed79e8857fb0
special characters
diff -r a88f12177e6f -r f8ac93c41720 helper.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/helper.R Tue Mar 20 13:59:04 2018 -0400
@@ -0,0 +1,28 @@
+#' \code{getopt_specification_matrix} returns a getopt specification matrix.
+#'
+#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
+#' The first column are short flags, the second column are argument masks, the third column
+#' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
+#' @param gtg_name the name of a running GTG.
+getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) {
+ df = read.csv(paste0(tool_dir, specification_file),
+ header = TRUE, stringsAsFactors = FALSE)
+ # check if there are duplicated short flags
+ short_flags = df[, 1]
+ if (length(unique(short_flags)) < length(short_flags)) {
+ cat('----Duplicated short flags found ----\n')
+ cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
+ stop('Duplicated short flags are not allowed.')
+ }
+
+ # use short flags to generate long flags
+ long_flags = paste0('X_', df[, 1])
+
+ # specification matrix
+ df2 = data.frame(long_flags = long_flags,
+ short_flags = df[, 1],
+ argument_mask = df[, 2],
+ data_type = df[, 3])
+
+ as.matrix(df2)
+}
\ No newline at end of file
diff -r a88f12177e6f -r f8ac93c41720 mygene_and_myvariant_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mygene_and_myvariant_macros.xml Tue Mar 20 13:59:04 2018 -0400
@@ -0,0 +1,1439 @@
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\ No newline at end of file
diff -r a88f12177e6f -r f8ac93c41720 variant_simple_search.Rmd
--- a/variant_simple_search.Rmd Tue Mar 20 11:29:28 2018 -0400
+++ b/variant_simple_search.Rmd Tue Mar 20 13:59:04 2018 -0400
@@ -19,12 +19,9 @@
# Code for computational analysis
-```{r 'step 1'}
-
-```
-
-```{r 'ste[ 2'}
-
+```{r}
+opt
```
+
diff -r a88f12177e6f -r f8ac93c41720 variant_simple_search.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_simple_search.csv Tue Mar 20 13:59:04 2018 -0400
@@ -0,0 +1,6 @@
+short flag,argument mask,data type,variable name,galaxy input type,description
+o,1,character,report,data,
+d,1,character,report.files_path,data,
+s,1,character,sink_message,text,
+q,1,character,variant_query,text,
+f,1,character,return_fields,text,
diff -r a88f12177e6f -r f8ac93c41720 variant_simple_search.xml
--- a/variant_simple_search.xml Tue Mar 20 11:29:28 2018 -0400
+++ b/variant_simple_search.xml Tue Mar 20 13:59:04 2018 -0400
@@ -1,30 +1,54 @@
-
-
+
+
some description
-
- pandocr-getoptr-rmarkdownr-jsonliter-dtr-curlr-rcurl
-
-
-
+ pandoc
+ r-getopt
+ r-rmarkdown
+ r-jsonlite
+ r-dt
+ r-curl
+ r-rcurl
+
+
+ mygene_and_myvariant_macros.xml
+
+
+
+
+
-
-
-
-
-
+
+
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+
+ ]]>
+
diff -r a88f12177e6f -r f8ac93c41720 variant_simple_search_render.R
--- a/variant_simple_search_render.R Tue Mar 20 11:29:28 2018 -0400
+++ b/variant_simple_search_render.R Tue Mar 20 13:59:04 2018 -0400
@@ -10,6 +10,8 @@
library(getopt)
library(rmarkdown)
+library(jsonlite)
+library(DT)
#------------------------------------------------
@@ -17,11 +19,11 @@
# load helper function
source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
# import getopt specification matrix from a csv file
-spec_csv = paste0(Sys.getenv('TOOL_DIR'), '/getopt_specification.csv')
-opt = getopt(getopt_specification_matrix(spec_csv))
+opt = getopt(getopt_specification_matrix('/variant_simple_search.csv'))
opt$X_t = Sys.getenv('TOOL_DIR')
#----------------------------------------------------
+print(opt)
#-----------using passed arguments in R
# to define system environment variables---
@@ -34,7 +36,7 @@
OUTPUT_DIR = opt$X_d
TOOL_DIR = opt$X_t
OUTPUT_REPORT = opt$X_o
-RMD_NAME = ''
+RMD_NAME = 'variant_simple_search.Rmd'
# create the output associated directory to store all outputs
dir.create(OUTPUT_DIR, recursive = TRUE)