Mercurial > repos > mingchen0919 > aurora_bdss_url
changeset 2:0d15928a648c draft
planemo upload for repository https://github.com/feltus/BDSS
| author | mingchen0919 |
|---|---|
| date | Mon, 11 Jun 2018 23:50:10 -0400 |
| parents | a110308993be |
| children | 9d42c3633b3f |
| files | build-and-run-job-scripts.sh rmarkdown_report.Rmd rmarkdown_report.xml |
| diffstat | 3 files changed, 5 insertions(+), 7 deletions(-) [+] |
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--- a/build-and-run-job-scripts.sh Mon Jun 11 23:40:40 2018 -0400 +++ b/build-and-run-job-scripts.sh Mon Jun 11 23:50:10 2018 -0400 @@ -3,12 +3,11 @@ mkdir download_dir #========== build and run bdss-download.sh script ============ -echo 'export PATH=/main/sites/galaxy/galaxy/tools/_conda/bin:$PATH' > bdss-download.sh - -echo 'for u in $(echo $X_u | sed "s/,/ /g");' >> bdss-download.sh +echo 'for u in $(echo $X_u | sed "s/,/ /g");' > bdss-download.sh echo 'do' >> bdss-download.sh echo ' bdss transfer --destination download_dir -u $u' >> bdss-download.sh echo 'done' >> bdss-download.sh +echo 'export PATH=/main/sites/galaxy/galaxy/tools/_conda/bin:$PATH' sh bdss-download.sh
--- a/rmarkdown_report.Rmd Mon Jun 11 23:40:40 2018 -0400 +++ b/rmarkdown_report.Rmd Mon Jun 11 23:50:10 2018 -0400 @@ -1,5 +1,5 @@ --- -title: 'Aurora Tool Report' +title: 'BDSS download report' output: html_document: highlight: pygments @@ -53,8 +53,6 @@ # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE --- -## BDSS download - ## Job script ```{bash, echo=FALSE}
--- a/rmarkdown_report.xml Mon Jun 11 23:40:40 2018 -0400 +++ b/rmarkdown_report.xml Mon Jun 11 23:50:10 2018 -0400 @@ -34,7 +34,8 @@ ]]></command> <inputs> - <param type="text" name="urls" area="true" size="5x25" label="URLs to data files" /> + <param type="text" name="urls" area="true" size="5x25" label="data URLs" + help="Multiple URLs should be separated with comma or space"/> </inputs> <outputs> <data format="html" name="report" label="${tool.name} report on ${on_string}"/>