# HG changeset patch
# User mingchen0919
# Date 1506546322 14400
# Node ID 627c487d22e32eea4741a6441d7fd2f52878c430
# Parent  61ab2acf020541b403adb85f4099e1713ba4d8f6
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty

diff -r 61ab2acf0205 -r 627c487d22e3 fastq_dump_pe.xml
--- a/fastq_dump_pe.xml	Wed Sep 27 17:00:42 2017 -0400
+++ b/fastq_dump_pe.xml	Wed Sep 27 17:05:22 2017 -0400
@@ -34,9 +34,9 @@
     <inputs>
         <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="false"
+        <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true"
                label="output files in fastq (true) or fasta (false)?"/>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="true"
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
                label="Display analysis code in report?"/>
     </inputs>
     <outputs>
diff -r 61ab2acf0205 -r 627c487d22e3 fastq_dump_pe_render.R
--- a/fastq_dump_pe_render.R	Wed Sep 27 17:00:42 2017 -0400
+++ b/fastq_dump_pe_render.R	Wed Sep 27 17:05:22 2017 -0400
@@ -43,7 +43,7 @@
 spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
 spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
 ##--------3. Rmd templates in the tool directory ----------
-spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character')
+spec_list$FASTQ_DUMP_PE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character')
 
 spec = t(as.data.frame(spec_list))
 opt = getopt(spec)