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diff test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular @ 16:c3e2a0805600 draft default tip

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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 13:47:50 +0000
parents 7f5d7b0e9884
children
line wrap: on
line diff
--- a/test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular	Sun Sep 08 06:59:19 2024 +0000
+++ b/test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular	Fri Nov 14 13:47:50 2025 +0000
@@ -1,31 +1,81 @@
-#custom_db
-#mpa_v21_CHOCOPhlAnxxx_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
+#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	52.20019	
-k__Bacteria|p__Actinobacteria	2|201174	34.37371	
-k__Bacteria|p__Firmicutes	2|1239	13.4261	
-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria	2|1224|1236	52.20019	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria	2|201174|1760	34.37371	
-k__Bacteria|p__Firmicutes|c__Bacilli	2|1239|91061	13.4261	
-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales	2|1224|1236|72274	52.20019	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales	2|201174|1760|85007	24.7409	
-k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales	2|1239|91061|186826	13.4261	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales	2|201174|1760|85009	9.63281	
-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae	2|1224|1236|72274|468	52.20019	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae	2|201174|1760|85007|1653	24.7409	
-k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae	2|1239|91061|186826|186828	13.4261	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae	2|201174|1760|85009|31957	9.63281	
-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella	2|1224|1236|72274|468|475	52.20019	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium	2|201174|1760|85007|1653|1716	24.7409	
-k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum	2|1239|91061|186826|186828|29393	13.4261	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium	2|201174|1760|85009|31957|1912216	9.63281	
-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata	2|1224|1236|72274|468|475|477	22.57968	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum	2|201174|1760|85007|1653|1716|37637	18.75365	
-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens	2|1224|1236|72274|468|475|478	15.88652	
-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi	2|1224|1236|72274|468|475|60442	13.73399	
-k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum	2|1239|91061|186826|186828|29393|29394	13.4261	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes	2|201174|1760|85009|31957|1912216|1747	9.63281	
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens	2|201174|1760|85007|1653|1716|38284	5.98726	
+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