# HG changeset patch
# User mingchen0919
# Date 1508187201 14400
# Node ID 58d48d1157ed9716c993274976c9374264804149
# Parent  cd86400bbaed97b6cef5c4ae863e19cace4d6237
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit b212086a85c4d1e62e0d0c0e77b6f3fcabea04ef-dirty

diff -r cd86400bbaed -r 58d48d1157ed fastq_dump_pe.Rmd
--- a/fastq_dump_pe.Rmd	Tue Oct 10 20:48:29 2017 -0400
+++ b/fastq_dump_pe.Rmd	Mon Oct 16 16:53:21 2017 -0400
@@ -30,7 +30,7 @@
 sra_accessions = sra_accessions[sra_accessions != '']
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
-  if('FORMAT' == 'fasta') {
+  if('FORMAT' == 'No') {
     command = paste0('fastq-dump --fasta --split-files ', '-O read_files_directory ', id)
   } else {
     command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id)
diff -r cd86400bbaed -r 58d48d1157ed fastq_dump_pe.xml
--- a/fastq_dump_pe.xml	Tue Oct 10 20:48:29 2017 -0400
+++ b/fastq_dump_pe.xml	Mon Oct 16 16:53:21 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="rmarkdown_fastq_dump_pe" name="fastq-dump-pe" version="1.0.0">
+<tool id="rmarkdown_fastq_dump_pe" name="fastq-dump-pe" version="1.0.1">
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
@@ -35,7 +35,7 @@
     <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="true"
+        <param type="boolean" name="format" truevalue="Yes" falsevalue="No" checked="true"
                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?"/>
diff -r cd86400bbaed -r 58d48d1157ed fastq_dump_se.Rmd
--- a/fastq_dump_se.Rmd	Tue Oct 10 20:48:29 2017 -0400
+++ b/fastq_dump_se.Rmd	Mon Oct 16 16:53:21 2017 -0400
@@ -30,7 +30,7 @@
 sra_accessions = sra_accessions[sra_accessions != '']
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
-  if('FORMAT' == 'fasta') {
+  if('FORMAT' == 'No') {
     command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id)
   } else {
     command = paste0('fastq-dump ', '-O read_files_directory ', id)
diff -r cd86400bbaed -r 58d48d1157ed fastq_dump_se.xml
--- a/fastq_dump_se.xml	Tue Oct 10 20:48:29 2017 -0400
+++ b/fastq_dump_se.xml	Mon Oct 16 16:53:21 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="rmarkdown_fastq_dump_se" name="fastq-dump-se" version="1.0.0">
+<tool id="rmarkdown_fastq_dump_se" name="fastq-dump-se" version="1.0.1">
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
@@ -35,7 +35,7 @@
     <inputs>
         <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="true" label="output files in fastq (Yes) or fasta (No)?"/>
+        <param type="boolean" name="format" truevalue="Yes" falsevalue="No" checked="true" 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>
     <outputs>