# HG changeset patch
# User mingchen0919
# Date 1506559412 14400
# Node ID dcd0e0b6fcaf4cd9499c31d651078fea1ffbc444
# Parent  cf1233051a9b23d25e29c0d9a987ae32bc2c78df
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit e6035405141d63626702084eacd02089f816cdc7-dirty

diff -r cf1233051a9b -r dcd0e0b6fcaf fastq_dump_pe.Rmd
--- a/fastq_dump_pe.Rmd	Wed Sep 27 17:12:39 2017 -0400
+++ b/fastq_dump_pe.Rmd	Wed Sep 27 20:43:32 2017 -0400
@@ -33,7 +33,7 @@
   if('FORMAT' == 'fasta') {
     command = paste0('fastq-dump --fasta --split_files ', '-O read_files_directory ')
   } else {
-    command = paste0('fastq-dump --fastq --split_files ', '-O read_files_directory ')
+    command = paste0('fastq-dump --split_files ', '-O read_files_directory ')
   }
   
   print(command)
@@ -47,6 +47,6 @@
 old_files = paste0('./read_files_directory/', list.files('./read_files_directory'))
 new_files = gsub('_1', '_forward', old_files)
 new_files = gsub('_2', '_reverse', new_files)
-file.copy('./read_files_directory/')
+file.rename(old_files, new_files)
 ```
 
diff -r cf1233051a9b -r dcd0e0b6fcaf fastq_dump_pe.xml
--- a/fastq_dump_pe.xml	Wed Sep 27 17:12:39 2017 -0400
+++ b/fastq_dump_pe.xml	Wed Sep 27 20:43:32 2017 -0400
@@ -36,7 +36,7 @@
         <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false"
                help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
         <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true"
-               label="output files in fastq (true) or fasta (false)?"/>
+               label="output files in fastq (Yes) or fasta (No)?"/>
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
                label="Display analysis code in report?"/>
     </inputs>