Mercurial > repos > iuc > extract_metaphlan_database
comparison test-data/SRS014464-Anterior_nares-abundances.tabular @ 0:5b2f8b6a3609 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
| author | iuc |
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| date | Mon, 19 Apr 2021 20:55:20 +0000 |
| parents | |
| children | 97ad0d817a45 |
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| -1:000000000000 | 0:5b2f8b6a3609 |
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| 1 #custom_db | |
| 2 #/home/bebatut/miniconda3/envs/mulled-v1-b4915a464cf72db4053ec566c65e3f5f431691323f08f9b6b1c9ecfc4f8b9c88/bin/metaphlan in --input_type fasta --read_min_len 70 --bowtie2db ref_db/ --index custom_db --bt2_ps very-sensitive --min_mapq_val 5 -t rel_ab --tax_lev a --min_cu_len 2000 --add_viruses --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmptu3575j7/files/000/dataset_19.dat --bowtie2out bowtie2out -s /tmp/tmptu3575j7/files/000/dataset_21.dat --biom /tmp/tmptu3575j7/files/000/dataset_22.dat --nproc 1 | |
| 3 #SampleID Metaphlan_Analysis | |
| 4 #clade_name NCBI_tax_id relative_abundance additional_species | |
| 5 k__Bacteria 2 100.0 | |
| 6 k__Bacteria|p__Proteobacteria 2|1224 52.20019 | |
| 7 k__Bacteria|p__Actinobacteria 2|201174 34.37371 | |
| 8 k__Bacteria|p__Firmicutes 2|1239 13.4261 | |
| 9 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 2|1224|1236 52.20019 | |
| 10 k__Bacteria|p__Actinobacteria|c__Actinobacteria 2|201174|1760 34.37371 | |
| 11 k__Bacteria|p__Firmicutes|c__Bacilli 2|1239|91061 13.4261 | |
| 12 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales 2|1224|1236|72274 52.20019 | |
| 13 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales 2|201174|1760|85007 24.7409 | |
| 14 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales 2|1239|91061|186826 13.4261 | |
| 15 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales 2|201174|1760|85009 9.63281 | |
| 16 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae 2|1224|1236|72274|468 52.20019 | |
| 17 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae 2|201174|1760|85007|1653 24.7409 | |
| 18 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae 2|1239|91061|186826|186828 13.4261 | |
| 19 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae 2|201174|1760|85009|31957 9.63281 | |
| 20 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella 2|1224|1236|72274|468|475 52.20019 | |
| 21 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium 2|201174|1760|85007|1653|1716 24.7409 | |
| 22 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum 2|1239|91061|186826|186828|29393 13.4261 | |
| 23 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium 2|201174|1760|85009|31957|1912216 9.63281 | |
| 24 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata 2|1224|1236|72274|468|475|477 22.57968 | |
| 25 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum 2|201174|1760|85007|1653|1716|37637 18.75365 | |
| 26 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens 2|1224|1236|72274|468|475|478 15.88652 | |
| 27 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi 2|1224|1236|72274|468|475|60442 13.73399 | |
| 28 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum 2|1239|91061|186826|186828|29393|29394 13.4261 | |
| 29 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes 2|201174|1760|85009|31957|1912216|1747 9.63281 | |
| 30 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens 2|201174|1760|85007|1653|1716|38284 5.98726 |