| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.9.9.0 (this tool) |
| humann2 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| humann2 | 0.9.9 | package |
| bowtie2 | 2.3.0 | package |
| metaphlan2 | 2.6.0 | package |
| diamond | 0.8.24 | package |
| rapsearch | 2.24 | package |
| python | 2.7.10 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
adv|identity_threshold: 50 adv|annotation_gene_index: 8 adv|prescreen_threshold: 0.01 nucleotide_db|nucleotide_database: list collection translated_alignment: diamond adv|output_max_dec: 10 adv|remove_column_description_output: False adv|translated_query_coverage_threshold: 50 bypass|bypass_prescreen: False adv|minpath: True pathways: metacyc search_mode: uniref50 protein_db|protein_db_selector: history bypass|bypass_translated_search: False adv|remove_statified_output: False adv|evalue: 1 adv|pick_frames: True adv|xipe: False bypass|bypass_nucleotide_search: False protein_db|protein_database: reduced_uniref50.fasta adv|output_format: tsv nucleotide_db|nucleotide_db_selector: history taxo_profile|taxonomic_profile_test: true adv|gap_fill: False bypass|bypass_nucleotide_index: False taxo_profile|taxonomic_profile: taxonomic_profile.tabular input: input_sequences.fasta adv|translated_subject_coverage_threshold: 50 |
gene_families_tsv: None pathcoverage_tsv: None pathabundance_tsv: None |
input_sequences.fasta taxonomic_profile.tabular g__Bacteroides.s__Bacteroides_stercoris.centroids.v0.1.1.ffn.gz g__Bacteroides.s__Bacteroides_thetaiotaomicron.centroids.v0.1.1.ffn.gz reduced_uniref50.fasta |
| Test-2 |
adv|identity_threshold: 50 adv|annotation_gene_index: 8 adv|prescreen_threshold: 0.01 nucleotide_db|nucleotide_database: list collection translated_alignment: rapsearch adv|translated_query_coverage_threshold: 50 adv|output_max_dec: 10 adv|remove_column_description_output: False taxo_profile|metaphlan2_db_choice|metaphlan2_db_selector: history bypass|bypass_prescreen: False taxo_profile|metaphlan2_db_choice|mpa_pkl: marker_metadata.json adv|minpath: True pathways: unipathway search_mode: uniref90 protein_db|protein_db_selector: history bypass|bypass_translated_search: False adv|remove_statified_output: False adv|evalue: 1 adv|pick_frames: True adv|xipe: False taxo_profile|metaphlan2_db_choice|bowtie2db: marker_sequences.fasta bypass|bypass_nucleotide_search: False protein_db|protein_database: reduced_uniref50.fasta adv|output_format: tsv nucleotide_db|nucleotide_db_selector: history taxo_profile|taxonomic_profile_test: false adv|gap_fill: False bypass|bypass_nucleotide_index: False input: input_sequences.fasta adv|translated_subject_coverage_threshold: 50 |
gene_families_tsv: None pathcoverage_tsv: None pathabundance_tsv: None |
input_sequences.fasta marker_sequences.fasta marker_metadata.json g__Bacteroides.s__Bacteroides_stercoris.centroids.v0.1.1.ffn.gz g__Bacteroides.s__Bacteroides_thetaiotaomicron.centroids.v0.1.1.ffn.gz reduced_uniref50.fasta |