# HG changeset patch
# User mingchen0919
# Date 1506394585 14400
# Node ID a5dcb110f21321ef708421591e04471ab268aa4c
# Parent  2f6a7c67440fb8e1a130db39ef6de64aedcbde36
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty

diff -r 2f6a7c67440f -r a5dcb110f213 collection_list.xml
--- a/collection_list.xml	Mon Sep 25 22:47:21 2017 -0400
+++ b/collection_list.xml	Mon Sep 25 22:56:25 2017 -0400
@@ -38,8 +38,9 @@
     </command>
     <inputs>
         <param type="data" name="file_list" multiple="true" />
+        <param type="text" name="format" label="the format 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?" />
-        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
     </inputs>
     <outputs>
         <data format="html" name="report" label="Collection builder (list collection)" />
diff -r 2f6a7c67440f -r a5dcb110f213 collection_list_paired.Rmd
--- a/collection_list_paired.Rmd	Mon Sep 25 22:47:21 2017 -0400
+++ b/collection_list_paired.Rmd	Mon Sep 25 22:56:25 2017 -0400
@@ -37,7 +37,7 @@
 # get original file names
 original_files = list.files('./files_directory')
 # create new files names from original file names
-new_files = gsub('\\.dat', '\\.FORMAT_1', original_files)
+new_files = gsub('\\.dat', '_1\\.FORMAT', original_files)
 # rename files
 file.copy(paste0('./files_directory/', original_files),
           paste0('./files_directory/', new_files))
@@ -47,13 +47,13 @@
 
 ```{r 'rename reverse files'}
 # get full paths of original files
-from_files = strsplit("FOWARD_FILE_LIST", ',')[[1]]
+from_files = strsplit("REVERSE_FILE_LIST", ',')[[1]]
 # copy files to the created directory.
 file.copy(from_files, './files_directory')
 # get original file names
 original_files = list.files('./files_directory')
 # create new files names from original file names
-new_files = gsub('\\.dat', '\\.FORMAT_2', original_files)
+new_files = gsub('\\.dat', '_2\\.FORMAT', original_files)
 # rename files
 file.copy(paste0('./files_directory/', original_files),
           paste0('./files_directory/', new_files))
diff -r 2f6a7c67440f -r a5dcb110f213 collection_list_paired.xml
--- a/collection_list_paired.xml	Mon Sep 25 22:47:21 2017 -0400
+++ b/collection_list_paired.xml	Mon Sep 25 22:56:25 2017 -0400
@@ -40,8 +40,9 @@
     <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="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="Collection builder (list:paired collection)" />