changeset 9:a9f93a4742b1 draft

update

--- a/extract_fields.xml	Fri Feb 23 14:34:05 2018 -0500
+++ b/extract_fields.xml	Fri Feb 23 15:42:48 2018 -0500
@@ -5,6 +5,7 @@
     <requirement type="package" version="1.3">r-rmarkdown</requirement>
     <requirement type="package" version="0.3.5">r-htmltools</requirement>
     <requirement type="package" version="0.5.0">r-dplyr</requirement>
+    <requirement type="package" version="v0.9.8">xorg-libxrender</requirement>
   </requirements>
   <description>some descriptions about the tool.</description>
   <stdio>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_template.Rmd	Fri Feb 23 15:42:48 2018 -0500
@@ -0,0 +1,14 @@
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+
+## Including Plots
+
+You can also embed plots, for example:
+
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

--- a/tool_template_render.R	Fri Feb 23 14:34:05 2018 -0500
+++ b/tool_template_render.R	Fri Feb 23 15:42:48 2018 -0500
@@ -17,9 +17,6 @@
 opt = getopt::getopt(spec_matrix)
 opt
 
-# build command: awk '{print $1,$2}' > output.txt and run
-X_A = paste0(paste0('$', trimws(strsplit(opt$X_A, ',')[[1]])), collapse = ',')
-extract_field_command = paste0("awk '{print ", X_A, " }' ", opt$X_B, " > ", opt$X_O)
-system(command = extract_field_command)
+rmarkdown::render(input = opt$X_t, output_file = opt$X_O)
 
 sink()