# HG changeset patch
# User mingchen0919
# Date 1506561356 14400
# Node ID 42e154ba2d350048576604244a51f6fcc55e2b81
# Parent  dcd0e0b6fcaf4cd9499c31d651078fea1ffbc444
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c4beda20972367ab7d47a058a01a5f6fe492255d-dirty

diff -r dcd0e0b6fcaf -r 42e154ba2d35 fastq_dump_pe.Rmd
--- a/fastq_dump_pe.Rmd	Wed Sep 27 20:43:32 2017 -0400
+++ b/fastq_dump_pe.Rmd	Wed Sep 27 21:15:56 2017 -0400
@@ -31,16 +31,25 @@
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
   if('FORMAT' == 'fasta') {
-    command = paste0('fastq-dump --fasta --split_files ', '-O read_files_directory ')
+    command = paste0('fastq-dump --fasta --split-files ', '-O read_files_directory ', id)
   } else {
-    command = paste0('fastq-dump --split_files ', '-O read_files_directory ')
+    command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id)
   }
-  
-  print(command)
-  system(command = command)
 }
 ```
 
+* `fastq-dump` command
+```{r}
+print(command)
+```
+
+* `command line stdout`
+
+```{r}
+system(command = command, intern = TRUE)
+```
+
+
 # Rename files
 
 ```{r}
diff -r dcd0e0b6fcaf -r 42e154ba2d35 fastq_dump_pe.xml
--- a/fastq_dump_pe.xml	Wed Sep 27 20:43:32 2017 -0400
+++ b/fastq_dump_pe.xml	Wed Sep 27 21:15:56 2017 -0400
@@ -42,7 +42,7 @@
     </inputs>
     <outputs>
         <data format="html" name="report" label="Fastq-dump report" />
-        <collection type="list" name="list_collection" label="Fastq-dump (paired end reads)">
+        <collection type="list:paired" name="list_collection" label="Fastq-dump (paired end reads)">
             <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="read_files_directory"/>
         </collection>
         <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" />
diff -r dcd0e0b6fcaf -r 42e154ba2d35 fastq_dump_pe_render.R
--- a/fastq_dump_pe_render.R	Wed Sep 27 20:43:32 2017 -0400
+++ b/fastq_dump_pe_render.R	Wed Sep 27 21:15:56 2017 -0400
@@ -54,7 +54,6 @@
 library(dplyr)
 
 #----- 1. create the report directory ------------------------
-# system(paste0('mkdir -p ', opt$output_dir))
 dir.create(opt$output_dir)
 
 #----- 2. generate Rmd files with Rmd templates --------------
diff -r dcd0e0b6fcaf -r 42e154ba2d35 fastq_dump_se.Rmd
--- a/fastq_dump_se.Rmd	Wed Sep 27 20:43:32 2017 -0400
+++ b/fastq_dump_se.Rmd	Wed Sep 27 21:15:56 2017 -0400
@@ -35,8 +35,17 @@
   } else {
     command = paste0('fastq-dump ', '-O read_files_directory ', id)
   }
-  print(command)
-  system(command = command)
 }
 ```
 
+* `fastq-dump` command
+```{r}
+print(command)
+```
+
+* `command line stdout`
+
+```{r}
+system(command = command, intern = TRUE)
+```
+
diff -r dcd0e0b6fcaf -r 42e154ba2d35 fastq_dump_se_render.R
--- a/fastq_dump_se_render.R	Wed Sep 27 20:43:32 2017 -0400
+++ b/fastq_dump_se_render.R	Wed Sep 27 21:15:56 2017 -0400
@@ -54,7 +54,7 @@
 library(dplyr)
 
 #----- 1. create the report directory ------------------------
-system(paste0('mkdir -p ', opt$output_dir))
+dir.create(opt$output_dir)
 
 #----- 2. generate Rmd files with Rmd templates --------------
 #   a. templates without placeholder variables: