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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan commit 26cbf16569d13b7ddbbbd99fc49ec15ce312a992
author iuc
date Fri, 14 Nov 2025 13:48:12 +0000
parents 97ad0d817a45
children
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#test-db
#/home/ubuntu/miniconda3/envs/__metaphlan@4.2.4/bin/metaphlan in --input_type fasta --read_min_len 70 --bt2_ps sensitive --min_mapq_val 5 --db_dir /home/ubuntu/Documents/glxy/git/tools-iuc/tools/metaphlan/test-data/test-db --index test-db -t rel_ab --tax_lev a --stat avg_g --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmpm9x253n7/job_working_directory/000/7/outputs/dataset_98364280-d229-4257-888e-ac290df6e8ca.dat --mapout mapout -s /tmp/tmpm9x253n7/job_working_directory/000/7/outputs/dataset_a8ceac4e-3f7c-47e6-bcc3-084f104ca1d8.dat --nproc 1 --offline
#17695 reads processed
#SampleID	Metaphlan_Analysis
#clade_name	NCBI_tax_id	relative_abundance	additional_species
UNCLASSIFIED	-1	0.0	
k__Bacteria	2	100.0	
k__Bacteria|p__Proteobacteria	2|1224	40.77283	
k__Bacteria|p__Firmicutes	2|1239	33.30552	
k__Bacteria|p__Actinobacteria	2|201174	23.9357	
k__Bacteria|p__Bacteroidetes	2|976	1.98596	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria	2|1224|1236	40.77283	
k__Bacteria|p__Firmicutes|c__Bacilli	2|1239|91061	33.30552	
k__Bacteria|p__Actinobacteria|c__Actinobacteria	2|201174|1760	23.9357	
k__Bacteria|p__Bacteroidetes|c__Bacteroidia	2|976|200643	1.98596	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales	2|1224|1236|72274	40.77283	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales	2|1239|91061|186826	33.30552	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales	2|201174|1760|85009	16.85816	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales	2|201174|1760|85007	7.07754	
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales	2|976|200643|171549	1.98596	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae	2|1224|1236|72274|468	40.77283	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae	2|1239|91061|186826|186828	29.38877	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae	2|201174|1760|85009|31957	16.85816	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae	2|201174|1760|85007|1653	7.07754	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae	2|1239|91061|186826|186827	3.91675	
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae	2|976|200643|171549|171552	1.98596	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella	2|1224|1236|72274|468|475	40.77283	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum	2|1239|91061|186826|186828|29393	29.38877	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium	2|201174|1760|85009|31957|1912216	16.85816	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium	2|201174|1760|85007|1653|1716	7.07754	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella	2|1239|91061|186826|186827|13075	3.91675	
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella	2|976|200643|171549|171552|838	1.98596	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum	2|1239|91061|186826|186828|29393|29394	29.38877	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes	2|201174|1760|85009|31957|1912216|1747	16.85816	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens	2|1224|1236|72274|468|475|478	11.04599	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi	2|1224|1236|72274|468|475|60442	9.86276	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_caprae	2|1224|1236|72274|468|475|90240	7.62178	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata	2|1224|1236|72274|468|475|477	4.28841	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis	2|1239|91061|186826|186827|13075|13076	3.91675	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum	2|201174|1760|85007|1653|1716|37637	3.25437	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_pluranimalium	2|1224|1236|72274|468|475|470453	2.85431	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_ovis	2|1224|1236|72274|468|475|29433	2.5544	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_catarrhalis	2|1224|1236|72274|468|475|480	2.54518	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens	2|201174|1760|85007|1653|1716|38284	2.44888	
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_timonensis	2|976|200643|171549|171552|838|386414	1.98596	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudogenitalium	2|201174|1760|85007|1653|1716|38303	1.3743	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi|t__GCA_002027555	2|1224|1236|72274|468|475|60442|	8.13478	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_caprae|t__GCA_900453285	2|1224|1236|72274|468|475|90240|	7.62178	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_000245815	2|1239|91061|186826|186828|29393|29394|	5.70862	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens|t__GCA_001679155	2|1224|1236|72274|468|475|478|	4.79602	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata|t__GCA_001679225	2|1224|1236|72274|468|475|477|	4.28841	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis|t__GCA_002847845	2|1239|91061|186826|186827|13075|13076|	3.91675	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_002572775	2|201174|1760|85009|31957|1912216|1747|	3.84553	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens|t__GCA_001679125	2|1224|1236|72274|468|475|478|	3.69469	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264045	2|1239|91061|186826|186828|29393|29394|	3.39602	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264065	2|1239|91061|186826|186828|29393|29394|	3.28678	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum|t__GCA_000466825	2|201174|1760|85007|1653|1716|37637|	3.25437	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003263975	2|1239|91061|186826|186828|29393|29394|	3.23401	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_003384345	2|201174|1760|85009|31957|1912216|1747|	3.00006	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_pluranimalium|t__GCA_002014825	2|1224|1236|72274|468|475|470453|	2.85431	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_001660855	2|201174|1760|85009|31957|1912216|1747|	2.57775	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens|t__GCA_001679005	2|1224|1236|72274|468|475|478|	2.55528	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_ovis|t__GCA_900453155	2|1224|1236|72274|468|475|29433|	2.5544	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264145	2|1239|91061|186826|186828|29393|29394|	2.55209	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_catarrhalis|t__GCA_000193085	2|1224|1236|72274|468|475|480|	2.54518	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003263915	2|1239|91061|186826|186828|29393|29394|	2.44642	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264015	2|1239|91061|186826|186828|29393|29394|	2.42412	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000144045	2|201174|1760|85009|31957|1912216|1747|	2.16928	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000302515	2|201174|1760|85009|31957|1912216|1747|	2.09203	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264135	2|1239|91061|186826|186828|29393|29394|	2.07154	
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_timonensis|t__GCA_000177055	2|976|200643|171549|171552|838|386414|	1.98596	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003263965	2|1239|91061|186826|186828|29393|29394|	1.82646	
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi|t__GCA_900453335	2|1224|1236|72274|468|475|60442|	1.72798	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_003384285	2|201174|1760|85009|31957|1912216|1747|	1.43296	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens|t__GCA_000146485	2|201174|1760|85007|1653|1716|38284|	1.41285	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudogenitalium|t__GCA_000156615	2|201174|1760|85007|1653|1716|38303|	1.3743	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264005	2|1239|91061|186826|186828|29393|29394|	1.30558	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000144005	2|201174|1760|85009|31957|1912216|1747|	1.18889	
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264085	2|1239|91061|186826|186828|29393|29394|	1.13712	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens|t__GCA_000159115	2|201174|1760|85007|1653|1716|38284|	1.03602	
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_001481615	2|201174|1760|85009|31957|1912216|1747|	0.55165