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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
author bgruening
date Wed, 23 Jul 2025 07:50:03 +0000
parents e5ecfffcfe45
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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1 #!/usr/bin/env python
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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3 import sys
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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5 import pandas as pd
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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8 def tabular_to_csv(tabular_file, csv_file):
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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9 """Convert tabular (TSV) to CSV"""
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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10 data = pd.read_csv(tabular_file, sep="\t")
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f413f828ef30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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11 if data.columns[0] == '' or data.columns[0].startswith('Unnamed:'):
f413f828ef30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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12 data.columns = ['ID'] + list(data.columns[1:])
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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13 data.to_csv(csv_file, index=False)
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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16 def csv_to_tabular(csv_file, tabular_file):
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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17 """Convert CSV to tabular (TSV)"""
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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18 data = pd.read_csv(csv_file)
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f413f828ef30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
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19 if data.columns[0] == '' or data.columns[0].startswith('Unnamed:'):
f413f828ef30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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20 data.columns = ['ID'] + list(data.columns[1:])
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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21 data.to_csv(tabular_file, sep="\t", index=False)
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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24 if __name__ == "__main__":
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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25 input_file = sys.argv[1]
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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26 output_file = sys.argv[2]
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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28 if input_file.endswith('.csv'):
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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29 csv_to_tabular(input_file, output_file)
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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30 else:
e5ecfffcfe45 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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31 tabular_to_csv(input_file, output_file)