Mercurial > repos > mvdbeek > add_input_name_as_column

annotate add_input_name_as_column.py @ 7:8061668d0868 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
author iuc
date Tue, 14 Oct 2025 17:13:02 +0000
parents 3284b72eef56
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
1 import argparse
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
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2 import io
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3a1f8302302d Imported from capsule None
mvdbeek
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3
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06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
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4
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3a1f8302302d Imported from capsule None
mvdbeek
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5 def Parser():
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06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
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6 the_parser = argparse.ArgumentParser(description="add label to last column of file")
7
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
7 the_parser.add_argument(
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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8 "--input", required=True, action="store", type=str, help="input tabular file"
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
9 )
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
10 the_parser.add_argument(
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
11 "--output", required=True, action="store", type=str, help="output file path"
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
12 )
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
13 the_parser.add_argument(
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
14 "--label",
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
15 required=True,
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
16 action="store",
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
17 type=str,
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
18 help="label to add in last column",
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
19 )
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
20 the_parser.add_argument(
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
21 "--header", action="store", type=str, help="column label for last column"
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
22 )
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
diff changeset
23 the_parser.add_argument(
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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24 "--prepend",
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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25 action="store_true",
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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26 default=False,
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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27 help="Prepend column instead of appending",
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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28 )
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3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
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06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
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30 args = the_parser.parse_args()
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
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31 return args
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3a1f8302302d Imported from capsule None
mvdbeek
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32
3a1f8302302d Imported from capsule None
mvdbeek
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5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
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34 args = Parser()
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
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06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
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8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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37 with io.open(args.input, encoding="utf-8") as input, io.open(
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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38 args.output, "w", encoding="utf-8"
8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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39 ) as output:
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06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
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40 for i, line in enumerate(input):
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8061668d0868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 1775d01920f27931a1935e233766f615d753502b
iuc
parents: 6
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41 line = line.strip("\n")
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
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42 if (i == 0) and args.header:
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3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
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43 new_entry = args.header
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
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44 else:
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3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
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45 new_entry = args.label
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
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46 if args.prepend:
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
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47 line = "%s\t%s\n" % (new_entry, line)
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
48 else:
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
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49 line = "%s\t%s\n" % (line, new_entry)
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
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50 output.write(line)