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improve csv_to_galaxy

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This commit is contained in:
Déborah Servili 2017-01-30 14:41:47 +01:00
parent 4ec941b18f
commit 5b68ec56db
1 changed files with 9 additions and 6 deletions
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17
tools/csv_to_galaxy.py
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@ -10,10 +10,10 @@ if __name__ == '__main__':
parser = argparse.ArgumentParser(description='CSV to Galaxy')
parser.add_argument("-c", "--csv", required=True, help="input csv")
parser.add_argument("-v", "--value", type=int, required=True, help="number of the column with the value")
parser.add_argument("-e", "--value_description", type=int, help="number of the column with description, if not defined, all other data wil be concataned")
parser.add_argument("-e", "--value_description", type=int, nargs='+', help="number of the column with description, if not defined, all other data wil be concataned")
parser.add_argument("-w", "--version", type=int, help="version of the galaxy")
parser.add_argument("-d", "--description", help="description of the galaxy")
parser.add_argument("-a", "--author", help="author of the galaxy")
parser.add_argument("-a", "--authors", nargs='+', help="author of the galaxy")
parser.add_argument("-s", "--source", help="source of the galaxy")
parser.add_argument("-t", "--type", help="type of galaxy, also the name of the generated json")
parser.add_argument("-n", "--name", help="name of the galaxy")
@ -33,10 +33,11 @@ if __name__ == '__main__':
continue
temp = {}
temp["value"] = data[args.value]
if args.value_description is not None:
temp["description"] = data[args.value_description]
else:
temp["description"] = ""
if args.value_description is not None:
for i in args.value_description:
temp["description"] = temp["description"] + data[i].replace('\n', ' ') + "; "
else:
for i in range(len(data)):
if i != args.value and data[i] != "":
temp["description"] = temp["description"] + data[i] + "; "
@ -57,8 +58,10 @@ if __name__ == '__main__':
else:
galaxy["description"] = "automagically generated galaxy"
if args.author is not None:
galaxy["authors"] = [args.author]
if args.authors is not None:
galaxy["authors"] = []
for author in args.authors:
galaxy["authors"].append(author)
else:
galaxy["authors"] = ["authorname"]