changeset 0:2f72cbded1d1 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_merge_rmarkdown.Rmd	Thu Dec 28 01:08:56 2017 -0500
@@ -0,0 +1,29 @@
+---
+title: 'HTML report title'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO,
+  error = TRUE
+)
+```
+
+
+# Code for computational analysis
+
+```{r 'step 1'}
+
+```
+
+```{r 'ste[ 2'}
+
+```
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_merge_rmarkdown.xml	Thu Dec 28 01:08:56 2017 -0500
@@ -0,0 +1,40 @@
+<tool id="rmarkdown_merge_rmarkdown" name="Merge R Markdown" version="1.0.0">
+  <requirements>
+    <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+    <requirement type="package" version="1.20.0">r-getopt</requirement>
+    <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>
+  </requirements>
+  <description>Merge multiple R Markdown files to generate one single report</description>
+  <stdio>
+    <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
+  </stdio>
+  <command><![CDATA[                    Rscript '${__tool_directory__}/rmarkdown_merge_rmarkdown_render.R'
+                        -e $echo
+                        -r $report
+                        -d $report.files_path
+                        -s $sink_message
+                        -t '${__tool_directory__}/rmarkdown_merge_rmarkdown.Rmd'
+                    ]]></command>
+  <inputs>
+    <param type="integer" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
+    <param type="data" name="rmarkdown_files" label="R Markdown files" optional="False" format="Rmd" multiple="True"/>
+  </inputs>
+  <outputs>
+    <data name="report" format="html" label="tool name report" hidden="false"/>
+    <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
+  </outputs>
+  <help><![CDATA[some help text]]></help>
+  <citations>
+    <citation><![CDATA[
+                    @article{allaire2016rmarkdown,
+                        title={rmarkdown: Dynamic Documents for R, 2016},
+                        author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+                        and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+                        journal={R package version 0.9},
+                        volume={6},
+                        year={2016}
+                    ]]></citation>
+  </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_merge_rmarkdown_render.R	Thu Dec 28 01:08:56 2017 -0500
@@ -0,0 +1,77 @@
+library(getopt)
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file('warnings_and_errors.txt')
+sink(zz)
+sink(zz, type = 'message')
+  ##---------below is the code for rendering .Rmd templates-----
+
+  ##=============STEP 1: handle command line arguments==========
+  ##
+  ##============================================================
+  # column 1: the long flag name
+  # column 2: the short flag alias. A SINGLE character string
+  # column 3: argument mask
+  #           0: no argument
+  #           1: argument required
+  #           2: argument is optional
+  # column 4: date type to which the flag's argument shall be cast.
+  #           possible values: logical, integer, double, complex, character.
+  #-------------------------------------------------------------
+  #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
+  # 1. short flag alias should match the flag in the command section in the XML file.
+  # 2. long flag name can be any legal R variable names
+  # 3. two names in args_list can have common string but one name should not be a part of another name.
+  #    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
+  #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+  args_list=list()
+  ##------- 1. input data ---------------------
+  args_list$ECHO = c('echo', 'e', '1', 'character')
+  ##--------2. output report and outputs --------------
+  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
+  args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
+  args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
+  ##--------3. .Rmd templates in the tool directory ----------
+  args_list$TOOL_TEMPLATE_RMD = c('rmarkdown_merge_rmarkdown_rmd', 't', '1', 'character')
+  ##-----------------------------------------------------------
+  opt = getopt(t(as.data.frame(args_list)))
+
+
+
+  ##=======STEP 2: create report directory (optional)==========
+  ##
+  ##===========================================================
+  dir.create(opt$report_dir)
+
+  ##=STEP 3: replace placeholders in .Rmd with argument values=
+  ##
+  ##===========================================================
+  #++ need to replace placeholders with args values one by one+
+  readLines(opt$rmarkdown_merge_rmarkdown_rmd) %>%
+    (function(x) {
+      gsub('ECHO', opt$echo, x)
+    }) %>%
+    (function(x) {
+      gsub('REPORT_DIR', opt$report_dir, x)
+    }) %>%
+    (function(x) {
+      fileConn = file('rmarkdown_merge_rmarkdown.Rmd')
+      writeLines(x, con=fileConn)
+      close(fileConn)
+    })
+
+
+  ##=============STEP 4: render .Rmd templates=================
+  ##
+  ##===========================================================
+  render('rmarkdown_merge_rmarkdown.Rmd', output_file = opt$report_html)
+
+
+  ##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================