Mercurial > repos > melissacline > xena_import
changeset 16:7f03b062f330 default tip
Cleaned up the user interface a bit
| author | melissacline |
|---|---|
| date | Tue, 23 Sep 2014 21:18:54 -0700 |
| parents | ff0cdac9636e |
| children | |
| files | xena_import.py xena_import.xml |
| diffstat | 2 files changed, 15 insertions(+), 3 deletions(-) [+] |
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--- a/xena_import.py Mon Sep 15 12:05:28 2014 -0700 +++ b/xena_import.py Tue Sep 23 21:18:54 2014 -0700 @@ -43,7 +43,12 @@ fp.close() # Finally, copy the genomic data into the Xena directory - shutil.copy(args.genomicDataPathname, xenaFileDir) + try: + shutil.copy(args.genomicDataPathname, xenaFileDir) + except: + print "Unexpected error", sys.exc_info()[0] + else: + print "Data copied successfully to Xena" if __name__ == "__main__": main()
--- a/xena_import.xml Mon Sep 15 12:05:28 2014 -0700 +++ b/xena_import.xml Tue Sep 23 21:18:54 2014 -0700 @@ -4,13 +4,20 @@ <requirement type="package" version="1.0">installXena</requirement> </requirements> <command interpreter="python"> - xena_import.py ${xenaInputData} ${cohort} ${metadataType} + xena_import.py ${xenaInputData} ${cohort} ${metadataType} > ${outfile} </command> <inputs> <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> - <param format="str" type="text" name="metadataType" label="Data Type (e.g. clinicalMatrix)" optional="false"/> + <param format="str" type="select" name="metadataType" label="File Format"> + <option value="genomicMatrix">Rows(Identifiers) by Columns (Samples)</option> + <option value="clinicalMatrix">Rows(Samples) by Columns (Identifiers)</option> + <option value="mutationVector">Mutation Data</option> + </param> </inputs> + <outputs> + <data foramt="txt" name="outfile"/> + </outputs> <help> To Appear </help>