# HG changeset patch
# User mingchen0919
# Date 1506364132 14400
# Node ID 78018b735124e10f5a43ea21fce2251554a77ca2

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty

diff -r 000000000000 -r 78018b735124 collection_list.Rmd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collection_list.Rmd	Mon Sep 25 14:28:52 2017 -0400
@@ -0,0 +1,29 @@
+---
+title: 'Collection builder (collection type: list)'
+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
+)
+```
+
+```{r}
+str(opt)
+```
+
+
+```{bash 'copy data to working directory', echo=FALSE}
+mkdir files_directory
+# Copy uploaded data to the working directory
+for f in $(echo FILE_LIST | sed "s/,/ /g")
+do
+    cp $f ./files_directory
+done
+```
\ No newline at end of file
diff -r 000000000000 -r 78018b735124 collection_list.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collection_list.xml	Mon Sep 25 14:28:52 2017 -0400
@@ -0,0 +1,34 @@
+<tool id="rmarkdown_collection_list" name="Collection type: list" version="1.0.0">
+    <description>
+        Create a 'list' dataset collection from a set of files in Galaxy history.
+    </description>
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            Rscript '${__tool_directory__}/collection_list_render.R'
+                -l $file_list
+                -e $echo
+
+                -r $report
+                -o $list_collection
+                -d $list_collection.files_path
+
+                -t '${__tool_directory__}/collection_list.Rmd'
+        ]]>
+    </command>
+    <inputs>
+        <param type="data" name="file_list" multiple="true" />
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data format="html" name="report" label="fastqc report" />
+        <collection type="list" name="list_collection">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="files_directory" />
+        </collection>
+    </outputs>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 78018b735124 collection_list_list.xml
diff -r 000000000000 -r 78018b735124 collection_list_render.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collection_list_render.R	Mon Sep 25 14:28:52 2017 -0400
@@ -0,0 +1,79 @@
+##======= Handle arguments from command line ========
+# setup R error handline to go to stderr
+options(show.error.messages=FALSE,
+        error=function(){
+          cat(geterrmessage(), file=stderr())
+          quit("no", 1, F)
+        })
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+# suppress warning
+options(warn = -1)
+
+options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
+args = commandArgs(trailingOnly=TRUE)
+
+suppressPackageStartupMessages({
+  library(getopt)
+  library(tools)
+})
+
+# 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.
+##------- 1. input data ---------------------
+spec_list=list()
+spec_list$FILE_LIST = c('file_list', 'l', '1', 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+##--------2. output report and outputs --------------
+spec_list$LIST_COLLECTION = c('list_collection', 'o', '1', 'character')
+spec_list$REPORT = c('report', 'r', '1', 'character')
+spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character')
+##--------3. Rmd templates in the tool directory ----------
+spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+##====== End of arguments handling ==========
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(htmltools)
+
+#----- 1. create the report directory ------------------------
+system(paste0('mkdir -p ', opt$list_collection_dir))
+
+#----- 2. generate Rmd files with Rmd templates --------------
+#   a. templates without placeholder variables:
+#         copy templates from tool directory to the working directory.
+#   b. templates with placeholder variables:
+#         substitute variables with user input values and place them in the working directory.
+
+#----- 01 list_collection.Rmd -----------------------
+readLines(opt$list_collection_rmd) %>%
+  (function(x) {
+    gsub('ECHO', opt$echo, x)
+  }) %>%
+  (function(x) {
+    gsub('FILE_LIST', opt$file_list, x)
+  }) %>%
+  (function(x) {
+    gsub('OUTPUT_DIR', opt$list_collection_dir, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('list_collection.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+#------ 3. render all Rmd files --------
+render('list_collection.Rmd', output_file = opt$list_collection_html)
+
+#-------4. manipulate outputs -----------------------------
diff -r 000000000000 -r 78018b735124 collection_paired.xml