| Previous changeset 2:9e2df763086c (2021-07-15) Next changeset 4:26ccb678abc8 (2021-10-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 28d2a0cfcbb04d88b6e19a7d898a2bada3bce149" |
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modified:
ena_upload.xml process_xlsx.py |
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| diff -r 9e2df763086c -r 59bb6d34fca6 ena_upload.xml --- a/ena_upload.xml Thu Jul 15 20:12:34 2021 +0000 +++ b/ena_upload.xml Wed Aug 18 19:42:49 2021 +0000 |
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| @@ -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> |
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| diff -r 9e2df763086c -r 59bb6d34fca6 process_xlsx.py --- a/process_xlsx.py Thu Jul 15 20:12:34 2021 +0000 +++ b/process_xlsx.py Wed Aug 18 19:42:49 2021 +0000 |
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| @@ -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(), |