Mercurial > repos > iuc > ena_upload
changeset 3:59bb6d34fca6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 28d2a0cfcbb04d88b6e19a7d898a2bada3bce149"
| author | iuc |
|---|---|
| date | Wed, 18 Aug 2021 19:42:49 +0000 |
| parents | 9e2df763086c |
| children | 26ccb678abc8 |
| files | ena_upload.xml process_xlsx.py |
| diffstat | 2 files changed, 9 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/ena_upload.xml Thu Jul 15 20:12:34 2021 +0000 +++ b/ena_upload.xml Wed Aug 18 19:42:49 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="ena_upload" name="ENA Upload tool" version="0.3.2" profile="20.01" license="MIT"> +<tool id="ena_upload" name="ENA Upload tool" version="0.3.3" profile="20.01" license="MIT"> <macros> <token name="@VERSION@">0.3.1</token> <import>samples_macros.xml</import>
--- a/process_xlsx.py Thu Jul 15 20:12:34 2021 +0000 +++ b/process_xlsx.py Wed Aug 18 19:42:49 2021 +0000 @@ -209,9 +209,13 @@ hour = "{:02d}".format(hour) minute = "{:02d}".format(minute) second = "{:02d}".format(second) - # format it as 2008-01-23T19:23:10 - sample[optional_col] = str(year) + '-' + str(month) + '-' + str(day) + \ - 'T' + str(hour) + ':' + str(minute) + ':' + str(second) + if optional_col in ('collection date'): + # collection date uses the format 2008-01-23T19:23:10 + sample[optional_col] = str(year) + '-' + str(month) + '-' + str(day) + \ + 'T' + str(hour) + ':' + str(minute) + ':' + str(second) + if optional_col in ('receipt date'): + # receipt date uses forma: 2008-01-23 + sample[optional_col] = str(year) + '-' + str(month) + '-' + str(day) # excel stores everything as float so I need to check if # the value was actually an int and keep it as int if isinstance(sample[optional_col], float): @@ -226,10 +230,9 @@ # (not listed in the samples or study dict) # process the experiments for this sample if exp['sample_alias'] == sample_alias: - lib_alias = 'library_' + exp_alias + '_' + exp['sample_alias'] experiments_table.write('\t'.join([exp_alias, action, 'accession_ena', exp['title'], exp['study_alias'], sample_alias, - exp['design_description'], lib_alias, + exp['design_description'], exp['library_name'], exp['library_strategy'], exp['library_source'], exp['library_selection'], exp['library_layout'].lower(),