# HG changeset patch
# User mingchen0919
# Date 1506362624 14400
# Node ID f85a6bcf940e663d372dbd79745550516c374fe2
# Parent  87c21e14f221b6df3164a46e72de264cce8d40b0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty

diff -r 87c21e14f221 -r f85a6bcf940e collection_list.Rmd
--- a/collection_list.Rmd	Mon Sep 25 12:15:23 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 14:03:44 2017 -0400
@@ -17,3 +17,13 @@
 ```{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 87c21e14f221 -r f85a6bcf940e collection_list.xml
--- a/collection_list.xml	Mon Sep 25 12:15:23 2017 -0400
+++ b/collection_list.xml	Mon Sep 25 14:03:44 2017 -0400
@@ -16,6 +16,7 @@
 
                 -r $report
                 -o $list_collection
+                -d $list_collection.files_path
 
                 -t '${__tool_directory__}/collection_list.Rmd'
         ]]>
@@ -26,6 +27,8 @@
     </inputs>
     <outputs>
         <data format="html" name="report" label="fastqc report" />
-        <collection type="list" name="list_collection" />
+        <collection type="list" name="list_collection">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="files_directory" />
+        </collection>
     </outputs>
 </tool>
\ No newline at end of file
diff -r 87c21e14f221 -r f85a6bcf940e collection_list_render.R
--- a/collection_list_render.R	Mon Sep 25 12:15:23 2017 -0400
+++ b/collection_list_render.R	Mon Sep 25 14:03:44 2017 -0400
@@ -30,11 +30,12 @@
 #           possible values: logical, integer, double, complex, character.
 ##------- 1. input data ---------------------
 spec_list=list()
-spec_list$READS = c('file_list', 'l', '1', 'character')
+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')
 
@@ -47,7 +48,7 @@
 library(htmltools)
 
 #----- 1. create the report directory ------------------------
-# this tool does not require an report directory
+system(paste0('mkdir -p ', opt$list_collection_dir))
 
 #----- 2. generate Rmd files with Rmd templates --------------
 #   a. templates without placeholder variables:
@@ -61,6 +62,12 @@
     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)