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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sat, 04 Nov 2023 18:59:48 +0000
parents 01ac9954c27f
children
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#mpa_vOct22_CHOCOPhlAnSGB_202212
#/usr/local/tools/_conda/envs/__metaphlan@4.0.6/bin/metaphlan /data/dnb08/galaxy_db/files/3/4/6/dataset_3461ff07-1b4d-4e57-b746-40d9d8066f01.dat,/data/dnb08/galaxy_db/files/e/a/b/dataset_eab63cfc-85ed-4f05-a3eb-f87cb309da27.dat --input_type fastq --read_min_len 70 --bt2_ps very-sensitive --min_mapq_val 5 --bowtie2db /data/db/data_managers/metaphlan/data/mpa_vOct22_CHOCOPhlAnSGB_202212 --index mpa_vOct22_CHOCOPhlAnSGB_202212 -t rel_ab --tax_lev a --min_cu_len 2000 --add_viruses --stat_q 0.1 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /data/jwd05e/main/059/485/59485896/outputs/galaxy_dataset_dbfb8cc7-14d1-4318-a3b7-2a988fa2ff7f.dat --bowtie2out bowtie2out -s /data/jwd05e/main/059/485/59485896/outputs/galaxy_dataset_1afff43f-1b78-4574-b961-e7c7e7b902f2.dat --biom /data/jwd05e/main/059/485/59485896/outputs/galaxy_dataset_f4980675-ac4a-44fa-9e21-4c33652e5e87.dat --nproc 1
#465754 reads processed
#SampleID	Metaphlan_Analysis
#clade_name	NCBI_tax_id	relative_abundance	additional_species
k__Bacteria	2	100.0	
k__Bacteria|p__Firmicutes	2|1239	68.23371	
k__Bacteria|p__Coprothermobacterota	2|2138240	31.76629	
k__Bacteria|p__Firmicutes|c__Clostridia	2|1239|186801	68.23371	
k__Bacteria|p__Coprothermobacterota|c__Coprothermobacteria	2|2138240|2138243	31.76629	
k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales	2|1239|186801|186802	68.23371	
k__Bacteria|p__Coprothermobacterota|c__Coprothermobacteria|o__Coprothermobacterales	2|2138240|2138243|2138246	31.76629	
k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae	2|1239|186801|186802|216572	68.23371	
k__Bacteria|p__Coprothermobacterota|c__Coprothermobacteria|o__Coprothermobacterales|f__Coprothermobacteraceae	2|2138240|2138243|2138246|2138247	31.76629	
k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio	2|1239|186801|186802|216572|35829	68.23371	
k__Bacteria|p__Coprothermobacterota|c__Coprothermobacteria|o__Coprothermobacterales|f__Coprothermobacteraceae|g__Coprothermobacter	2|2138240|2138243|2138246|2138247|68335	31.76629	
k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio_thermocellus	2|1239|186801|186802|216572|35829|1515	68.23371	
k__Bacteria|p__Coprothermobacterota|c__Coprothermobacteria|o__Coprothermobacterales|f__Coprothermobacteraceae|g__Coprothermobacter|s__Coprothermobacter_proteolyticus	2|2138240|2138243|2138246|2138247|68335|35786	31.76629	
k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio_thermocellus|t__SGB8476	2|1239|186801|186802|216572|35829|1515|	68.23371	
k__Bacteria|p__Coprothermobacterota|c__Coprothermobacteria|o__Coprothermobacterales|f__Coprothermobacteraceae|g__Coprothermobacter|s__Coprothermobacter_proteolyticus|t__SGB8555	2|2138240|2138243|2138246|2138247|68335|35786|	31.76629