changeset 50:3a2154271930 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b33359f9f0ca5bb3227050b4b586a9969c7e20ad-dirty

--- a/collection_paired.Rmd	Tue Sep 26 13:12:19 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
----
-title: 'Build collection: a paired datasets'
-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
-
-```{r}
-file.copy("FORWARD_INPUT", './OUTPUT_DIR/forward.FORMAT')
-file.copy("REVERSE_INPUT", './OUTPUT_DIR/reverse.FORMAT')
-```
-

--- a/collection_paired.xml	Tue Sep 26 13:12:19 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<tool id="rmarkdown_collection_paired" name="Collection type (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 paired dataset collection from files in 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_paired_render.R'
-                -L $forward_input
-                -R $reverse_input
-                -e $echo
-                -f $format
-
-                -r $report
-                -d $report.files_path
-
-                -t '${__tool_directory__}/collection_paired.Rmd'
-        ]]>
-    </command>
-    <inputs>
-        <param type="data" name="forward_input" multiple="false" label="forward input"/>
-        <param type="data" name="reverse_input" multiple="false" label="reverse input"/>
-        <param type="text" name="format" label="the format (extension) 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 (paired collection)" />
-        <collection type="paired" name="list_collection">
-        </collection>
-    </outputs>
-</tool>
\ No newline at end of file

--- a/collection_paired_render.R	Tue Sep 26 13:12:19 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-##======= 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$FORWARD_INPUT = c('forward_input', 'L', '1', 'character')
-spec_list$REVERSE_INPUT = c('reverse_input', '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$OUTPUT_HTML = c('paired_collection_html', 'r', '1', 'character')
-spec_list$OUTPUT_DIR = c('paired_collection_dir', 'd', '1', 'character')
-##--------3. Rmd templates in the tool directory ----------
-spec_list$PAIRED_COLLECTION_RMD = c('paired_collection_rmd', 't', '1', 'character')
-
-spec = t(as.data.frame(spec_list))
-opt = getopt(spec)
-##====== End of arguments handling ==========
-
-#------ Load libraries ---------
-library(rmarkdown)
-library(htmltools)
-library(dplyr)
-
-#----- 1. create the report directory ------------------------
-system(paste0('mkdir -p ', opt$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 paired_collection.Rmd -----------------------
-readLines(opt$paired_collection_rmd) %>%
-  (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
-    gsub('FORMAT', opt$format, x)
-  }) %>%
-  (function(x) {
-    gsub('FORWARD_INPUT', opt$forward_input, x)
-  }) %>%
-  (function(x) {
-    gsub('REVERSE_INPUT', opt$reverse_input, x)
-  }) %>%
-  (function(x) {
-    gsub('OUTPUT_DIR', opt$paired_collection_dir, x)
-  }) %>%
-  (function(x) {
-    fileConn = file('paired_collection.Rmd')
-    writeLines(x, con=fileConn)
-    close(fileConn)
-  })
-
-#------ 3. render all Rmd files --------
-render('paired_collection.Rmd', output_file = opt$paired_collection_html)
-
-
-#-------4. manipulate outputs -----------------------------