Mercurial > repos > mingchen0919 > aurora_fasta_importer
changeset 2:3d4f21a85f68 draft
planemo upload
| author | mingchen0919 |
|---|---|
| date | Tue, 15 May 2018 08:26:40 -0400 |
| parents | dfd29c07d6ca |
| children | 2c8c06250531 |
| files | build-and-run-job-scripts.sh command-line-arguments.csv rmarkdown_report.xml |
| diffstat | 3 files changed, 7 insertions(+), 11 deletions(-) [+] |
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--- a/build-and-run-job-scripts.sh Tue May 15 00:52:51 2018 -0400 +++ b/build-and-run-job-scripts.sh Tue May 15 08:26:40 2018 -0400 @@ -3,11 +3,10 @@ #========== build and run job 1 script ============ cat >curl-download.sh <<EOF -if [ "$X_f" != 'None' ];then +if [[ $(wc -l <$X_f) -ge 2 ]];then cp $X_f $X_O -elif [ "$X_u" != "TRUE" ];then - curl $X_u > $X_O -fi +else + curl $(head -1 $X_f) > $X_O EOF # run job 1 script
--- a/command-line-arguments.csv Tue May 15 00:52:51 2018 -0400 +++ b/command-line-arguments.csv Tue May 15 08:26:40 2018 -0400 @@ -2,6 +2,5 @@ o,1,character,report d,1,character,report.files_path f,1,character,upload_fasta -u,2,character,url_fasta O,1,character,output_fasta
--- a/rmarkdown_report.xml Tue May 15 00:52:51 2018 -0400 +++ b/rmarkdown_report.xml Tue May 15 08:26:40 2018 -0400 @@ -30,19 +30,17 @@ -d $report.files_path -f $upload_fasta - -u $url_fasta -O $output_fasta ]]></command> <inputs> - <param type="data" name="upload_fasta" format="fa,fna,fasta" label="Fasta file from history" - optional="True"/> - <param type="text" name="url_fasta" label="URL to downloadable fasta file"/> + <param type="data" name="upload_fasta" format="txt,fa,fna,fasta" label="Fasta file or Fasta URL" + help="A fasta file or a txt file. If it is txt file, it should only has one line, which is an URL to a downloadable fasta file."/> </inputs> <outputs> - <data format="html" name="report" label="${tool.name} report on ${on_string}" /> - <data format="fasta" name="output_fasta" label="${tool.name} fasta on ${on_string}" /> + <data format="html" name="report" label="${tool.name} report on ${on_string}"/> + <data format="fasta" name="output_fasta" label="${tool.name} fasta"/> </outputs> <citations> <citation type="bibtex"><![CDATA[