# HG changeset patch
# User mingchen0919
# Date 1506545647 14400
# Node ID 66bc1016ec2afac0427cc284f5ef7df77768f8d7
# Parent  d330ce2d4663a3a4dc44789bc50a29bd7963c4d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty

diff -r d330ce2d4663 -r 66bc1016ec2a fastq_dump_pe.Rmd
--- a/fastq_dump_pe.Rmd	Wed Sep 27 16:49:22 2017 -0400
+++ b/fastq_dump_pe.Rmd	Wed Sep 27 16:54:07 2017 -0400
@@ -31,16 +31,11 @@
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
   if('FORMAT' == 'fasta') {
-    command = paste0('fastq-dump --fasta ', '-O read_files_directory ')
+    command = paste0('fastq-dump --fasta --split_files ', '-O read_files_directory ')
   } else {
-    command = paste0('fastq-dump ', '-O read_files_directory ')
+    command = paste0('fastq-dump --fastq --split_files ', '-O read_files_directory ')
   }
   
-  if('SPLIT_FILES' == TRUE) {
-    command = paste0(command, '--split_files ', id)
-  } else {
-    command = paste0(command, id)
-  }
   print(command)
   system(command = command)
 }
diff -r d330ce2d4663 -r 66bc1016ec2a fastq_dump_pe.xml
--- a/fastq_dump_pe.xml	Wed Sep 27 16:49:22 2017 -0400
+++ b/fastq_dump_pe.xml	Wed Sep 27 16:54:07 2017 -0400
@@ -8,7 +8,7 @@
         <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
     </requirements>
     <description>
-        Download and extract single end reads in fastq or fasta format from NCBI SRA. The output is a list of datasets
+        Download and extract paired end reads in fastq or fasta format from NCBI SRA. The output is a list of paired datasets
         collection.
     </description>
     <stdio>
@@ -27,7 +27,6 @@
                 -p $split_files
 
                 -r $report
-                -d $report.files_path
                 -s $sink_message
 
                 -t '${__tool_directory__}/fastq_dump_pe.Rmd'
@@ -38,9 +37,6 @@
                help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
         <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="false"
                label="output files in fastq (true) or fasta (false)?"/>
-        <param type="boolean" name="split_files" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Split files"
-               help="Dump each read into separate file. Files will receive suffix corresponding to read number"/>
-
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
                label="Display analysis code in report?"/>
     </inputs>
diff -r d330ce2d4663 -r 66bc1016ec2a fastq_dump_pe_render.R
--- a/fastq_dump_pe_render.R	Wed Sep 27 16:49:22 2017 -0400
+++ b/fastq_dump_pe_render.R	Wed Sep 27 16:54:07 2017 -0400
@@ -38,11 +38,10 @@
 spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
 spec_list$FORMAT = c('format', 'f', '1', 'character')
 spec_list$ECHO = c('echo', 'e', '1', 'character')
-spec_list$SPLIT_FILES = c('split_files', 'p', '1', 'character')
 ##--------2. output report and outputs --------------
 spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
 spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
-spec_list$SINK_OUTPUT = c('sink_output', 's', '1', 'character')
+spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
 ##--------3. Rmd templates in the tool directory ----------
 spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character')
 
@@ -75,9 +74,6 @@
     gsub('ECHO', opt$echo, x)
   }) %>%
   (function(x) {
-    gsub('SPLIT_FILES', opt$split_files, x)
-  }) %>%
-  (function(x) {
     gsub('OUTPUT_DIR', opt$output_dir, x)
   }) %>%
   (function(x) {
diff -r d330ce2d4663 -r 66bc1016ec2a fastq_dump_se_render.R
--- a/fastq_dump_se_render.R	Wed Sep 27 16:49:22 2017 -0400
+++ b/fastq_dump_se_render.R	Wed Sep 27 16:54:07 2017 -0400
@@ -41,7 +41,7 @@
 ##--------2. output report and outputs --------------
 spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
 spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
-spec_list$SINK_OUTPUT = c('sink_output', 's', '1', 'character')
+spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
 ##--------3. Rmd templates in the tool directory ----------
 spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_se_rmd', 't', '1', 'character')