annotate format_metaphlan2_output.py @ 2:370b56f8a02d draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
author bgruening
date Wed, 19 Oct 2022 14:39:16 +0000
parents 1e74cb2c8e67
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
1 #!/usr/bin/env python
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
2 # -*- coding: utf-8 -*-
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
3
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
4 import argparse
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
5
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
6
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
7 taxo_level_corresp = {
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
8 "k": "kingdom",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
9 "p": "phylum",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
10 "c": "class",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
11 "o": "order",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
12 "f": "family",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
13 "g": "genus",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
14 "s": "species",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
15 "t": "strains",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
16 }
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
17
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
18
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
19 def write_taxo_abundance(output_files, level, taxo, abundance):
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
20 if level not in taxo_level_corresp:
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
21 raise ValueError(level + " is not a know taxonomic level")
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
22 f_n = taxo_level_corresp[level]
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
23 output_files[f_n].write(taxo + "\t")
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
24 output_files[f_n].write(abundance + "\n")
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
25
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
26
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
27 def format_metaphlan2_output(args):
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
28 taxo_levels_abund_f = {
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
29 "kingdom": open(args.kingdom_abundance_file, "w"),
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
30 "phylum": open(args.phylum_abundance_file, "w"),
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
31 "class": open(args.class_abundance_file, "w"),
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
32 "order": open(args.order_abundance_file, "w"),
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
33 "family": open(args.family_abundance_file, "w"),
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
34 "genus": open(args.genus_abundance_file, "w"),
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
35 "species": open(args.species_abundance_file, "w"),
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
36 "strains": open(args.strains_abundance_file, "w"),
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
37 }
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
38
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
39 for taxo_level_f in taxo_levels_abund_f:
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
40 s = taxo_level_f + "\t" + "abundance\n"
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
41 taxo_levels_abund_f[taxo_level_f].write(s)
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
42
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
43 with open(args.metaphlan2_output, "r") as input_f:
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
44 with open(args.all_taxo_level_abundance_file, "w") as output_f:
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
45 s = "kingdom\tphylum\tclass\torder\tfamily\t"
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
46 s += "genus\tspecies\tstrains\tabundance\n"
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
47 output_f.write(s)
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
48
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
49 levels_number = 8
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
50 for line in input_f.readlines():
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
51 if line.startswith("#"):
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
52 continue
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
53
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
54 split_line = line[:-1].split("\t")
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
55 all_taxo = split_line[0]
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
56 abundance = split_line[1]
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
57
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
58 split_taxo = all_taxo.split("|")
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
59 for level in split_taxo:
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
60 taxo = level.split("__")[1]
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
61 taxo = taxo.replace("_", " ")
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
62 output_f.write(taxo + "\t")
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
63
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
64 for i in range(len(split_taxo), levels_number):
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
65 output_f.write("\t")
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
66
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
67 output_f.write(abundance + "\n")
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
68
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
69 last_taxo_level = split_taxo[-1].split("__")
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
70 taxo = last_taxo_level[1].replace("_", " ")
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
71 level = last_taxo_level[0]
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
72 write_taxo_abundance(taxo_levels_abund_f, level, taxo, abundance)
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
73
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
74 for taxo_level_f in taxo_levels_abund_f:
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
75 taxo_levels_abund_f[taxo_level_f].close()
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
76
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
77
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
78 if __name__ == "__main__":
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
79 parser = argparse.ArgumentParser()
2
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
80 parser.add_argument("--metaphlan2_output", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
81 parser.add_argument("--all_taxo_level_abundance_file", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
82 parser.add_argument("--kingdom_abundance_file", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
83 parser.add_argument("--phylum_abundance_file", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
84 parser.add_argument("--class_abundance_file", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
85 parser.add_argument("--order_abundance_file", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
86 parser.add_argument("--family_abundance_file", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
87 parser.add_argument("--genus_abundance_file", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
88 parser.add_argument("--species_abundance_file", required=True)
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
89 parser.add_argument("--strains_abundance_file", required=True)
0
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
90 args = parser.parse_args()
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
parents:
diff changeset
91
1
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
diff changeset
92 format_metaphlan2_output(args)