Mercurial > repos > bebatut > format_metaphlan2_output

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sat, 04 Nov 2023 19:00:01 +0000
parents 370b56f8a02d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
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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
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2 # -*- coding: utf-8 -*-
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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4 import argparse
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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7 taxo_level_corresp = {
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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8 "k": "kingdom",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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9 "p": "phylum",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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10 "c": "class",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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11 "o": "order",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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12 "f": "family",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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13 "g": "genus",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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14 "s": "species",
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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15 "t": "strains",
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16 }
370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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19 def write_taxo_abundance(output_files, level, taxo, abundance):
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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20 if level not in taxo_level_corresp:
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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21 raise ValueError(level + " is not a know taxonomic level")
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22 f_n = taxo_level_corresp[level]
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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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"
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24 output_files[f_n].write(abundance + "\n")
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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27 def format_metaphlan2_output(args):
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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28 taxo_levels_abund_f = {
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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"
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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"
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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"
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32 "order": open(args.order_abundance_file, "w"),
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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"
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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"
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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"
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36 "strains": open(args.strains_abundance_file, "w"),
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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37 }
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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39 for taxo_level_f in taxo_levels_abund_f:
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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40 s = taxo_level_f + "\t" + "abundance\n"
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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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"
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42
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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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"
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44 with open(args.all_taxo_level_abundance_file, "w") as output_f:
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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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"
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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"
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47 output_f.write(s)
1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
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49 levels_number = 8
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50 for line in input_f.readlines():
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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51 if line.startswith("#"):
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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52 continue
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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54 split_line = line[:-1].split("\t")
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55 all_taxo = split_line[0]
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56 abundance = split_line[1]
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58 split_taxo = all_taxo.split("|")
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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59 for level in split_taxo:
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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60 taxo = level.split("__")[1]
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61 taxo = taxo.replace("_", " ")
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62 output_f.write(taxo + "\t")
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64 for i in range(len(split_taxo), levels_number):
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65 output_f.write("\t")
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67 output_f.write(abundance + "\n")
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69 last_taxo_level = split_taxo[-1].split("__")
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70 taxo = last_taxo_level[1].replace("_", " ")
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71 level = last_taxo_level[0]
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72 write_taxo_abundance(taxo_levels_abund_f, level, taxo, abundance)
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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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"
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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"
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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78 if __name__ == "__main__":
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79 parser = argparse.ArgumentParser()
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370b56f8a02d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"
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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
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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
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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
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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
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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
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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
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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
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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
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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
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89 parser.add_argument("--strains_abundance_file", required=True)
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2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
bebatut
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90 args = parser.parse_args()
2bfa9b200600 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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91
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1e74cb2c8e67 "planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
bebatut
parents: 0
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92 format_metaphlan2_output(args)