# HG changeset patch
# User mingchen0919
# Date 1506371877 14400
# Node ID b4adc08beae70b196255154596b625b6ceca46dc
# Parent  26718249095fd8d90f325f56b44f61ed42e0fe6f
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 93b036c66fd754a7af459fa80d3f7f143a68477b-dirty

diff -r 26718249095f -r b4adc08beae7 collection_list.Rmd
--- a/collection_list.Rmd	Mon Sep 25 16:24:24 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 16:37:57 2017 -0400
@@ -20,6 +20,7 @@
 str(opt)
 ```
 
+# Rename files
 
 ```{r 'rename files'}
 # create directory
@@ -37,4 +38,3 @@
           paste0('./files_directory/', new_files))
 ```
 
-# End
diff -r 26718249095f -r b4adc08beae7 collection_list.xml
--- a/collection_list.xml	Mon Sep 25 16:24:24 2017 -0400
+++ b/collection_list.xml	Mon Sep 25 16:37:57 2017 -0400
@@ -1,7 +1,4 @@
 <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>
@@ -9,6 +6,23 @@
         <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' 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 '${__tool_directory__}/collection_list_render.R'
diff -r 26718249095f -r b4adc08beae7 collection_list_render.R
--- a/collection_list_render.R	Mon Sep 25 16:24:24 2017 -0400
+++ b/collection_list_render.R	Mon Sep 25 16:37:57 2017 -0400
@@ -34,7 +34,7 @@
 spec_list$ECHO = c('echo', 'e', '1', 'character')
 spec_list$FORMAT = c('format', 'f', '1', 'character')
 ##--------2. output report and outputs --------------
-spec_list$REPORT = c('report', 'r', '1', 'character')
+spec_list$OUTPUT_HTML = c('list_collection_html', 'r', '1', 'character')
 spec_list$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')
@@ -78,6 +78,7 @@
   })
 
 #------ 3. render all Rmd files --------
-render('list_collection.Rmd', output_file = opt$report)
+render('list_collection.Rmd', output_file = opt$list_collection_html)
+
 
 #-------4. manipulate outputs -----------------------------