# HG changeset patch
# User mingchen0919
# Date 1522851026 14400
# Node ID 3c859d09407497309a22d613faa80755890b6139
# Parent  2167f32cf37974632c4f3ebd6325501c8cb190db
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e

diff -r 2167f32cf379 -r 3c859d094074 fastq_dump_pe.Rmd
--- a/fastq_dump_pe.Rmd	Wed Sep 27 21:38:54 2017 -0400
+++ b/fastq_dump_pe.Rmd	Wed Apr 04 10:10:26 2018 -0400
@@ -10,7 +10,7 @@
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(
-  echo = ECHO
+  echo = FALSE
 )
 ```
 
diff -r 2167f32cf379 -r 3c859d094074 fastq_dump_pe.xml
--- a/fastq_dump_pe.xml	Wed Sep 27 21:38:54 2017 -0400
+++ b/fastq_dump_pe.xml	Wed Apr 04 10:10:26 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rmarkdown_fastqc_dump_pe" name="fastqc-dump-pe" version="1.0.0">
+<tool id="rmarkdown_fastq_dump_pe" name="fastq-dump-pe" version="1.0.2">
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
@@ -22,7 +22,6 @@
         <![CDATA[
             Rscript '${__tool_directory__}/fastq_dump_pe_render.R'
                 -i '$sra_accession'
-                -e $echo
                 -f $format
 
                 -r $report
@@ -35,10 +34,10 @@
     <inputs>
         <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false"
                help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
-        <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true"
-               label="output files in fastq (Yes) or fasta (No)?"/>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
-               label="Display analysis code in report?"/>
+        <param type="select" name="format" label="Output format">
+            <option value="fastq" selected="true">fastq</option>
+            <option value="fasta">fasta</option>
+        </param>
     </inputs>
     <outputs>
         <data format="html" name="report" label="Fastq-dump report" />
diff -r 2167f32cf379 -r 3c859d094074 fastq_dump_pe_render.R
--- a/fastq_dump_pe_render.R	Wed Sep 27 21:38:54 2017 -0400
+++ b/fastq_dump_pe_render.R	Wed Apr 04 10:10:26 2018 -0400
@@ -37,7 +37,6 @@
 spec_list=list()
 spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
 spec_list$FORMAT = c('format', 'f', '1', 'character')
-spec_list$ECHO = c('echo', 'e', '1', 'character')
 ##--------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')
@@ -71,9 +70,6 @@
     gsub('FORMAT', opt$format, x)
   }) %>%
   (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
     gsub('OUTPUT_DIR', opt$output_dir, x)
   }) %>%
   (function(x) {
diff -r 2167f32cf379 -r 3c859d094074 fastq_dump_se.Rmd
--- a/fastq_dump_se.Rmd	Wed Sep 27 21:38:54 2017 -0400
+++ b/fastq_dump_se.Rmd	Wed Apr 04 10:10:26 2018 -0400
@@ -10,7 +10,7 @@
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(
-  echo = ECHO
+  echo = FALSE
 )
 ```
 
diff -r 2167f32cf379 -r 3c859d094074 fastq_dump_se.xml
--- a/fastq_dump_se.xml	Wed Sep 27 21:38:54 2017 -0400
+++ b/fastq_dump_se.xml	Wed Apr 04 10:10:26 2018 -0400
@@ -1,8 +1,8 @@
-<tool id="rmarkdown_fastqc_dump_se" name="fastqc-dump-se" version="1.0.0">
+<tool id="rmarkdown_fastq_dump_se" name="fastq-dump-se" version="1.0.2">
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
         <requirement type="package" version="0.3.5">r-htmltools</requirement>
         <requirement type="package" version="0.5.0">r-dplyr</requirement>
         <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
@@ -16,13 +16,12 @@
         <regex match="XXX"
                source="stderr"
                level="warning"
-               description="Check the warnings_and_errors.txt file for more details." />
+               description="Check the warnings_and_errors.txt file for more details."/>
     </stdio>
     <command>
         <![CDATA[
             Rscript '${__tool_directory__}/fastq_dump_se_render.R'
                 -i '$sra_accession'
-                -e $echo
                 -f $format
 
                 -r $report
@@ -35,14 +34,16 @@
     <inputs>
         <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions"
                help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
-        <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true" label="output files in fastq (Yes) or fasta (No)?"/>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+        <param type="select" name="format" label="Output format">
+            <option value="fastq" selected="true">fastq</option>
+            <option value="fasta">fasta</option>
+        </param>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="Fastq-dump report" />
+        <data format="html" name="report" label="Fastq-dump report"/>
         <collection type="list" name="list_collection" label="Fastq-dump (single end reads)">
-            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" />
+            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory"/>
         </collection>
-        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" />
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
     </outputs>
 </tool>
\ No newline at end of file
diff -r 2167f32cf379 -r 3c859d094074 fastq_dump_se_render.R
--- a/fastq_dump_se_render.R	Wed Sep 27 21:38:54 2017 -0400
+++ b/fastq_dump_se_render.R	Wed Apr 04 10:10:26 2018 -0400
@@ -37,7 +37,6 @@
 spec_list=list()
 spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
 spec_list$FORMAT = c('format', 'f', '1', 'character')
-spec_list$ECHO = c('echo', 'e', '1', 'character')
 ##--------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')
@@ -71,9 +70,6 @@
     gsub('FORMAT', opt$format, x)
   }) %>%
   (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
     gsub('OUTPUT_DIR', opt$output_dir, x)
   }) %>%
   (function(x) {