# HG changeset patch
# User mingchen0919
# Date 1522862497 14400
# Node ID 8e913d0be3e661ec1f796cc910e33d9ba8dc4dd2
# Parent  55b0c9de7057b1b23880ae6fd916d64395ae75e5
planemo upload

diff -r 55b0c9de7057 -r 8e913d0be3e6 fastq_dump_pe.Rmd
--- a/fastq_dump_pe.Rmd	Wed Apr 04 12:55:55 2018 -0400
+++ b/fastq_dump_pe.Rmd	Wed Apr 04 13:21:37 2018 -0400
@@ -10,21 +10,18 @@
 ```
 
 
-```{bash echo=FALSE}
+```{bash}
 # build job-script
 mkdir -p ${WORKING_DIR}/paired-end-reads
-```
 
-
-```{bash}
 # paired-end.sh
 mkdir -p ${X_d}/paired-end-reads
 cat <<EOF >${X_d}/paired-end.sh
-if [ "${X_B}" ];then
+if [ "${X_A}" ];then
   fastq-dump \\
     --split-files \\
-    ${X_B} \\
-    -O ${X_d}/paired-end-reads > ${X_d}/paired-end-log.txt 2>&1
+    ${X_A} \\
+    -O ${WORKING_DIR}/paired-end-reads > ${X_d}/paired-end-log.txt 2>&1
 else
   echo "No accessions are provided" > ${X_d}/paired-end-log.txt 2>&1
 fi
@@ -48,7 +45,7 @@
 
 
 ```{bash, 'display script', results='asis', echo=FALSE}
-echo '### paired-end reads'
+echo '## Job script'
 echo ''
 echo ''
 echo '```bash'
diff -r 55b0c9de7057 -r 8e913d0be3e6 fastq_dump_pe.xml
--- a/fastq_dump_pe.xml	Wed Apr 04 12:55:55 2018 -0400
+++ b/fastq_dump_pe.xml	Wed Apr 04 13:21:37 2018 -0400
@@ -31,7 +31,7 @@
               from_work_dir="warnings_and_errors.txt" hidden="false"/>
         <collection name="list_paired_collection" type="list:paired" label="${tool.name} list:paired collection">
             <discover_datasets
-                    pattern="(?P&amp;lt;identifier_0&amp;gt;[^_]+)_(?P&amp;lt;identifier_1&amp;gt;[^_]+)\.(?P&amp;lt;ext&amp;gt;[^\._]+)?"
+                    pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?"
                     directory="paired-end-reads" visible="false"/>
         </collection>
     </outputs>
diff -r 55b0c9de7057 -r 8e913d0be3e6 fastq_dump_pe_render.R
--- a/fastq_dump_pe_render.R	Wed Apr 04 12:55:55 2018 -0400
+++ b/fastq_dump_pe_render.R	Wed Apr 04 13:21:37 2018 -0400
@@ -36,7 +36,7 @@
 OUTPUT_DIR = opt$X_d
 TOOL_DIR =   opt$X_t
 OUTPUT_REPORT = opt$X_o
-RMD_NAME = 'fastq_dump.Rmd'
+RMD_NAME = 'fastq_dump_pe.Rmd'
 
 
 # create the output associated directory to store all outputs
diff -r 55b0c9de7057 -r 8e913d0be3e6 fastq_dump_se.Rmd
--- a/fastq_dump_se.Rmd	Wed Apr 04 12:55:55 2018 -0400
+++ b/fastq_dump_se.Rmd	Wed Apr 04 13:21:37 2018 -0400
@@ -10,12 +10,10 @@
 ```
 
 
-```{bash echo=FALSE}
+```{bash}
 # build job-script
 mkdir -p ${WORKING_DIR}/single-end-reads
-```
 
-```{bash}
 # single-end.sh
 cat <<EOF >${X_d}/single-end.sh
 if [ "${X_A}" ];then
@@ -39,8 +37,6 @@
 ```{bash, 'display script', results='asis', echo=FALSE}
 echo '## Job scripts'
 echo ''
-echo '### single-end reads'
-echo ''
 echo ''
 echo '```bash'
 cat ${X_d}/single-end.sh
diff -r 55b0c9de7057 -r 8e913d0be3e6 fastq_dump_se_render.R
--- a/fastq_dump_se_render.R	Wed Apr 04 12:55:55 2018 -0400
+++ b/fastq_dump_se_render.R	Wed Apr 04 13:21:37 2018 -0400
@@ -36,7 +36,7 @@
 OUTPUT_DIR = opt$X_d
 TOOL_DIR =   opt$X_t
 OUTPUT_REPORT = opt$X_o
-RMD_NAME = 'fastq_dump.Rmd'
+RMD_NAME = 'fastq_dump_se.Rmd'
 
 
 # create the output associated directory to store all outputs