changeset 13:ff1cb127967e draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty

--- a/collection_list.Rmd	Mon Sep 25 16:10:27 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 16:19:14 2017 -0400
@@ -16,22 +16,12 @@
 
 # Command line arguments
 
-```{r}
+```{r 'command line arguments'}
 str(opt)
 ```
 
 
-```{bash 'copy data to working directory'}
-mkdir files_directory
-# Copy uploaded data to the working directory
-for f in $(echo FILE_LIST | sed "s/,/ /g")
-do
-    sed "s/.dat/"
-    cp $f ./files_directory
-done
-```
-
-```{r}
+```{r 'rename files'}
 # create directory
 dir.create('./files_directory')
 # get full paths of original files
@@ -41,9 +31,10 @@
 # get original file names
 original_files = list.files('./files_directory')
 # create new files names from original file names
-new_files = gsub('\\.dat', '\\.fastqsanger', original_files)
+new_files = gsub('\\.dat', '\\.FORMAT', original_files)
 # rename files
 file.copy(paste0('./files_directory/', original_files),
           paste0('./files_directory/', new_files))
 ```
 
+# End

--- a/collection_list.xml	Mon Sep 25 16:10:27 2017 -0400
+++ b/collection_list.xml	Mon Sep 25 16:19:14 2017 -0400
@@ -14,6 +14,7 @@
             Rscript '${__tool_directory__}/collection_list_render.R'
                 -l $file_list
                 -e $echo
+                -f $format
 
                 -r $report
                 -d $report.files_path
@@ -24,6 +25,7 @@
     <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?" />
+        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
     </inputs>
     <outputs>
         <data format="html" name="report" label="fastqc report" />

--- a/collection_list_render.R	Mon Sep 25 16:10:27 2017 -0400
+++ b/collection_list_render.R	Mon Sep 25 16:19:14 2017 -0400
@@ -32,6 +32,7 @@
 spec_list=list()
 spec_list$FILE_LIST = c('file_list', 'l', '1', 'character')
 spec_list$ECHO = c('echo', 'e', '1', 'character')
+spec_list$FORMAT = c('echo', 'f', '1', 'character')
 ##--------2. output report and outputs --------------
 spec_list$REPORT = c('report', 'r', '1', 'character')
 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character')
@@ -62,6 +63,9 @@
     gsub('ECHO', opt$echo, x)
   }) %>%
   (function(x) {
+    gsub('FORMAT', opt$echo, x)
+  }) %>%
+  (function(x) {
     gsub('FILE_LIST', opt$file_list, x)
   }) %>%
   (function(x) {