# HG changeset patch
# User mingchen0919
# Date 1506399369 14400
# Node ID 66022ba24ac71fe4521601b4055403afd0b63620
# Parent  63e9500cdeec26fc9eb0efa677553ccb7b984e5f
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty

diff -r 63e9500cdeec -r 66022ba24ac7 collection_list.xml
--- a/collection_list.xml	Mon Sep 25 16:41:49 2017 -0400
+++ b/collection_list.xml	Tue Sep 26 00:16:09 2017 -0400
@@ -38,11 +38,12 @@
     </command>
     <inputs>
         <param type="data" name="file_list" multiple="true" />
+        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
+
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
-        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="Collection builder report" />
+        <data format="html" name="report" label="Collection builder (list collection)" />
         <collection type="list" name="list_collection">
             <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
         </collection>
diff -r 63e9500cdeec -r 66022ba24ac7 collection_list_list.xml
diff -r 63e9500cdeec -r 66022ba24ac7 collection_list_paired.Rmd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collection_list_paired.Rmd	Tue Sep 26 00:16:09 2017 -0400
@@ -0,0 +1,70 @@
+---
+title: 'Collection builder (collection type: list:paired)'
+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
+)
+```
+
+# Command line arguments
+
+```{r 'command line arguments'}
+str(opt)
+```
+
+# Rename files
+
+## Forward inputs
+
+```{r 'create inputs directory'}
+# create directory to store both forward and reverse inputs
+# this is the directory where datasets will be discovered.
+dir.create('./files_directory')
+```
+
+```{r 'rename forward files'}
+# create directory
+dir.create('./forward_files_directory')
+# get full paths of original files
+from_files = strsplit("FORWARD_FILE_LIST", ',')[[1]]
+# copy files to forward_files_directory.
+file.copy(from_files, './forward_files_directory')
+# get original file names
+original_files = list.files('./forward_files_directory')
+# create new files names from original file names
+new_files = gsub('\\.dat', '_forward\\.FORMAT', original_files)
+new_files = paste0('input_', 1:length(original_files), '_forward.FORMAT')
+new_files
+# rename files
+file.copy(paste0('./forward_files_directory/', original_files),
+          paste0('./files_directory/', new_files))
+```
+
+## Reverse inputs
+
+```{r 'rename reverse files'}
+# create directory
+dir.create('./reverse_files_directory')
+# get full paths of original files
+from_files = strsplit("REVERSE_FILE_LIST", ',')[[1]]
+# copy files to reverse_files_directory.
+file.copy(from_files, './reverse_files_directory')
+# get original file names
+original_files = list.files('./reverse_files_directory')
+# create new files names from original file names
+new_files = gsub('\\.dat', '_reverse\\.FORMAT', original_files)
+new_files = paste0('input_', 1:length(original_files), '_reverse.FORMAT')
+new_files
+# rename files
+file.copy(paste0('./reverse_files_directory/', original_files),
+          paste0('./files_directory/', new_files))
+```
+
diff -r 63e9500cdeec -r 66022ba24ac7 collection_list_paired.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collection_list_paired.xml	Tue Sep 26 00:16:09 2017 -0400
@@ -0,0 +1,53 @@
+<tool id="rmarkdown_collection_list_paired" name="Collection type: list:paired" 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="1.2">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>
+        Create a 'list:paired' dataset collection from a set of files in Galaxy history.
+    </description>
+    <stdio>
+        <regex match="Execution halted"
+               source="both"
+               level="fatal"
+               description="Execution halted." />
+        <regex match="Error in"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+        <regex match="Fatal error"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+    </stdio>
+    <command>
+        <![CDATA[
+            Rscript '${__tool_directory__}/collection_list_paired_render.R'
+                -L $forward_file_list
+                -R $reverse_file_list
+                -e $echo
+                -f $format
+
+                -r $report
+                -d $report.files_path
+
+                -t '${__tool_directory__}/collection_list_paired.Rmd'
+        ]]>
+    </command>
+    <inputs>
+        <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/>
+        <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/>
+        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
+
+        <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="Collection builder (list:paired collection)" />
+        <collection type="list:paired" name="list_collection">
+            <discover_datasets pattern="__name_and_ext__" directory="files_directory" visible="true"/>
+        </collection>
+    </outputs>
+</tool>
\ No newline at end of file
diff -r 63e9500cdeec -r 66022ba24ac7 collection_list_paired_render.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collection_list_paired_render.R	Tue Sep 26 00:16:09 2017 -0400
@@ -0,0 +1,85 @@
+##======= 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$FORWARD_FILE_LIST = c('forward_file_list', 'L', '1', 'character')
+spec_list$REVERSE_FILE_LIST = c('reverse_file_list', 'R', '1', 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+spec_list$FORMAT = c('format', 'f', '1', 'character')
+##--------2. output report and outputs --------------
+spec_list$OUTPUT_HTML = c('list_paired_collection_html', 'r', '1', 'character')
+spec_list$OUTPUT_DIR = c('list_paired_collection_dir', 'd', '1', 'character')
+##--------3. Rmd templates in the tool directory ----------
+spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+##====== End of arguments handling ==========
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+
+#----- 1. create the report directory ------------------------
+system(paste0('mkdir -p ', opt$list_paired_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('FORMAT', opt$format, x)
+  }) %>%
+  (function(x) {
+    gsub('FORWARD_FILE_LIST', opt$forward_file_list, x)
+  }) %>%
+  (function(x) {
+    gsub('REVERSE_FILE_LIST', opt$reverse_file_list, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('list_paired_collection.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+#------ 3. render all Rmd files --------
+render('list_paired_collection.Rmd', output_file = opt$list_paired_collection_html)
+
+
+#-------4. manipulate outputs -----------------------------