# HG changeset patch
# User mingchen0919
# Date 1506443061 14400
# Node ID fb05ca4741270e29c1d6b4d333578536747586df
# Parent  8dacd341b8b7a6fd57276548f39a2d45c9ed5a01
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit a7ad932a1725b4ef26d522040c5395ae0026fb35-dirty

diff -r 8dacd341b8b7 -r fb05ca474127 collection_list_paired.xml
--- a/collection_list_paired.xml	Tue Sep 26 12:10:20 2017 -0400
+++ b/collection_list_paired.xml	Tue Sep 26 12:24:21 2017 -0400
@@ -40,7 +40,7 @@
     <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="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>
diff -r 8dacd341b8b7 -r fb05ca474127 collection_paired.xml
--- a/collection_paired.xml	Tue Sep 26 12:10:20 2017 -0400
+++ b/collection_paired.xml	Tue Sep 26 12:24:21 2017 -0400
@@ -38,8 +38,8 @@
         ]]>
     </command>
     <inputs>
-        <param type="data" name="forward_input" multiple="true" label="forward input"/>
-        <param type="data" name="reverse_input" multiple="true" label="reverse input"/>
+        <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?" />
diff -r 8dacd341b8b7 -r fb05ca474127 collection_paired_render.R
--- a/collection_paired_render.R	Tue Sep 26 12:10:20 2017 -0400
+++ b/collection_paired_render.R	Tue Sep 26 12:24:21 2017 -0400
@@ -31,14 +31,14 @@
 ##------- 1. input data ---------------------
 spec_list=list()
 spec_list$FORWARD_INPUT = c('forward_input', 'L', '1', 'character')
-spec_list$REVERSE_INPUT = c('reverse_forward_input', 'R', '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$OUTPUT_DIR = c('paired_collection_dir', 'd', '1', 'character')
 ##--------3. Rmd templates in the tool directory ----------
-spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
+spec_list$PAIRED_COLLECTION_RMD = c('paired_collection_rmd', 't', '1', 'character')
 
 spec = t(as.data.frame(spec_list))
 opt = getopt(spec)
@@ -58,8 +58,8 @@
 #   b. templates with placeholder variables:
 #         substitute variables with user input values and place them in the working directory.
 
-#----- 01 list_collection.Rmd -----------------------
-readLines(opt$list_collection_rmd) %>%
+#----- 01 paired_collection.Rmd -----------------------
+readLines(opt$paired_collection_rmd) %>%
   (function(x) {
     gsub('ECHO', opt$echo, x)
   }) %>%