Mercurial > repos > mingchen0919 > aurora_fastq_dump
changeset 2:8e913d0be3e6 draft
planemo upload
author | mingchen0919 |
---|---|
date | Wed, 04 Apr 2018 13:21:37 -0400 |
parents | 55b0c9de7057 |
children | 668be0a63172 |
files | fastq_dump_pe.Rmd fastq_dump_pe.xml fastq_dump_pe_render.R fastq_dump_se.Rmd fastq_dump_se_render.R |
diffstat | 5 files changed, 9 insertions(+), 16 deletions(-) [+] |
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--- 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" > ${X_d}/paired-end-log.txt 2>&1 fi @@ -48,7 +45,7 @@ ```{bash, 'display script', results='asis', echo=FALSE} -echo '### paired-end reads' +echo '## Job script' echo '' echo '' echo '```bash'
--- a/fastq_dump_pe.xml Wed Apr 04 12:55:55 2018 -0400 +++ b/fastq_dump_pe.xml Wed Apr 04 13:21:37 2018 -0400 @@ -31,7 +31,7 @@ from_work_dir="warnings_and_errors.txt" hidden="false"/> <collection name="list_paired_collection" type="list:paired" label="${tool.name} list:paired collection"> <discover_datasets - pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" + pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" directory="paired-end-reads" visible="false"/> </collection> </outputs>
--- 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
--- 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 ${X_d}/single-end.sh
--- a/fastq_dump_se_render.R Wed Apr 04 12:55:55 2018 -0400 +++ b/fastq_dump_se_render.R Wed Apr 04 13:21:37 2018 -0400 @@ -36,7 +36,7 @@ OUTPUT_DIR = opt$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