# HG changeset patch
# User mingchen0919
# Date 1506525059 14400
# Node ID c9b56151f112d9f33d7d4bda9165412b56f91ce5
# Parent  dce9200ef1b7423d4cd002a7625fb23b46786132
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c9517f0b061cdca3b79678d9a2620e1e43115d42-dirty

diff -r dce9200ef1b7 -r c9b56151f112 fastq_dump_se.xml
--- a/fastq_dump_se.xml	Wed Sep 27 10:36:39 2017 -0400
+++ b/fastq_dump_se.xml	Wed Sep 27 11:10:59 2017 -0400
@@ -39,7 +39,7 @@
         ]]>
     </command>
     <inputs>
-        <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false"
+        <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions"
                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="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
diff -r dce9200ef1b7 -r c9b56151f112 fastq_dump_se_render.R
--- a/fastq_dump_se_render.R	Wed Sep 27 10:36:39 2017 -0400
+++ b/fastq_dump_se_render.R	Wed Sep 27 11:10:59 2017 -0400
@@ -59,7 +59,7 @@
 #----- 01 fastq_dump_se.Rmd -----------------------
 readLines(opt$fastq_dump_se_rmd) %>%
   (function(x) {
-    gsub('SRA_ACCESSION', opt$file_list, x)
+    gsub('SRA_ACCESSION', opt$sra_accession, x)
   }) %>%
   (function(x) {
     gsub('ECHO', opt$echo, x)