Mercurial > repos > recetox > matchms_formatter
changeset 1:364976b9aba6 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 67040e686204e86c07ec46ca90129e50e40eb737"
| author | recetox |
|---|---|
| date | Tue, 11 Jan 2022 15:13:57 +0000 |
| parents | 0a08bed94964 |
| children | 52abfe76c25b |
| files | formatter.py matchms_formatter.xml |
| diffstat | 2 files changed, 9 insertions(+), 6 deletions(-) [+] |
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--- a/formatter.py Sat Oct 30 13:48:25 2021 +0000 +++ b/formatter.py Tue Jan 11 15:13:57 2022 +0000 @@ -73,8 +73,8 @@ Returns: DataFrame: Joined dataframe on compounds containing scores an matches in long format. """ - matches = read_csv(matches_filename, sep='\t', index_col=0) - scores = read_csv(scores_filename, sep='\t', index_col=0) + matches = read_csv(matches_filename, sep=None, index_col=0) + scores = read_csv(scores_filename, sep=None, index_col=0) scores_long = create_long_table(scores, 'score') matches_long = create_long_table(matches, 'matches') @@ -113,8 +113,11 @@ @cli.resultcallback() def write_output(result: DataFrame, scores_filename, matches_filename, output_filename): + input_file = read_csv(scores_filename, sep=None, iterator=True) + sep = input_file._engine.data.dialect.delimiter + result = result.reset_index().rename(columns={'level_0': 'query', 'compound': 'reference'}) - result.to_csv(output_filename, sep="\t", index=False) + result.to_csv(output_filename, sep=sep, index=False) if __name__ == '__main__':
--- a/matchms_formatter.xml Sat Oct 30 13:48:25 2021 +0000 +++ b/matchms_formatter.xml Tue Jan 11 15:13:57 2022 +0000 @@ -31,8 +31,8 @@ </configfiles> <inputs> - <param label="Scores Table" name="scores" type="data" format="tsv" help="Scores output table." /> - <param label="Matches Table" name="matches" type="data" format="tsv" help="Scores output table." /> + <param label="Scores Table" name="scores" type="data" format="csv,tsv" help="Scores output table." /> + <param label="Matches Table" name="matches" type="data" format="csv,tsv" help="Scores output table." /> <conditional name="method"> <param name="selection" type="select" label="Formatting method"> @@ -52,7 +52,7 @@ </inputs> <outputs> - <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format="tsv" /> + <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format_source="scores" /> </outputs> <tests>