| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.6.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.0.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.0.0+galaxy0 |
| humann |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| humann | 3.0.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
in|input: demo.fastq.gz in|selector: raw wf|prescreen|metaphlan_db|bowtie2db: test-db/metaphlan-db/demo-db-v30.fasta wf|prescreen|metaphlan_db|mpa_pkl: test-db/metaphlan-db/demo-db-v30.json wf|prescreen|metaphlan_db|selector: history wf|prescreen|prescreen_threshold: 0.01 wf|nucleotide_search|nucleotide_db|nucleotide_database: list collection wf|nucleotide_search|nucleotide_db|selector: history wf|nucleotide_search|nucleotide_identity_threshold: 0 wf|nucleotide_search|nucleotide_subject_coverage_threshold: 50 wf|nucleotide_search|nucleotide_query_coverage_threshold: 90 wf|translated_search|protein_db|protein_database: test-db/protein-db/uniref90_demo_prots_v201901b.fasta wf|translated_search|protein_db|search_mode: uniref90 wf|translated_search|protein_db|selector: history wf|translated_search|evalue: 1 wf|translated_search|translated_subject_coverage_threshold: 50 wf|translated_search|translated_query_coverage_threshold: 90 wf|selector: none g_p_quant|gap_fill: True g_p_quant|minpath: True g_p_quant|pathways: metacyc g_p_quant|xipe: False g_p_quant|annotation_gene_index: 3 out|output_basename: humann out|output_format: tsv out|output_max_decimals: 10 out|remove_column_description_output: False out|intermediate_temp: ['metaphlan_bowtie2', 'metaphlan_bugs_list', 'bowtie2_alignment', 'bowtie2_reduced_alignment', 'bowtie2_unaligned', 'custom_chocophlan_database', 'diamond_aligned', 'diamond_unaligned'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
demo.fastq.gz test-db/metaphlan-db/demo-db-v30.fasta test-db/metaphlan-db/demo-db-v30.json test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v296_201901b.ffn.gz test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v296_201901b.ffn.gz test-db/protein-db/uniref90_demo_prots_v201901b.fasta value |
| Test-2 |
in|input: demo.fasta.gz in|selector: raw wf|nucleotide_search|nucleotide_db|nucleotide_database: chocophlan-DEMO-20210421 wf|nucleotide_search|nucleotide_db|selector: cached wf|nucleotide_search|nucleotide_identity_threshold: 0 wf|nucleotide_search|nucleotide_subject_coverage_threshold: 50 wf|nucleotide_search|nucleotide_query_coverage_threshold: 90 wf|translated_search|protein_db|protein_database: uniref-DEMO_diamond-20210421 wf|translated_search|protein_db|selector: cached wf|translated_search|evalue: 1 wf|translated_search|translated_subject_coverage_threshold: 50 wf|translated_search|translated_query_coverage_threshold: 90 wf|selector: bypass_prescreen g_p_quant|gap_fill: True g_p_quant|minpath: True g_p_quant|pathways: metacyc g_p_quant|xipe: False g_p_quant|annotation_gene_index: 3 out|output_basename: humann out|output_format: biom out|output_max_decimals: 10 out|remove_column_description_output: False out|intermediate_temp: |
name: value name: value name: value name: value |
demo.fasta.gz value |
| Test-3 |
in|input: demo.fasta.gz in|selector: raw wf|taxonomic_profile: demo-taxonomic-profile.tabular wf|nucleotide_search|nucleotide_db|nucleotide_database: chocophlan-DEMO-20210421 wf|nucleotide_search|nucleotide_db|selector: cached wf|nucleotide_search|nucleotide_identity_threshold: 0 wf|nucleotide_search|nucleotide_subject_coverage_threshold: 50 wf|nucleotide_search|nucleotide_query_coverage_threshold: 90 wf|translated_search|protein_db|protein_database: uniref-DEMO_diamond-20210421 wf|translated_search|protein_db|selector: cached wf|translated_search|evalue: 1 wf|translated_search|translated_subject_coverage_threshold: 50 wf|translated_search|translated_query_coverage_threshold: 90 wf|selector: bypass_taxonomic_profiling g_p_quant|gap_fill: True g_p_quant|minpath: True g_p_quant|pathways: metacyc g_p_quant|xipe: False g_p_quant|annotation_gene_index: 3 out|output_basename: humann out|output_format: tsv out|output_max_decimals: 10 out|remove_column_description_output: False out|intermediate_temp: |
name: value name: value name: value name: value |
demo.fasta.gz demo-taxonomic-profile.tabular value |
| Test-4 |
in|input: demo.sam in|selector: mapping wf|nucleotide_search|nucleotide_db|nucleotide_database: chocophlan-DEMO-20210421 wf|nucleotide_search|nucleotide_db|selector: cached wf|nucleotide_search|nucleotide_identity_threshold: 0 wf|nucleotide_search|nucleotide_subject_coverage_threshold: 50 wf|nucleotide_search|nucleotide_query_coverage_threshold: 90 wf|translated_search|protein_db|protein_database: uniref-DEMO_diamond-20210421 wf|translated_search|protein_db|selector: cached wf|translated_search|evalue: 1 wf|translated_search|translated_subject_coverage_threshold: 50 wf|translated_search|translated_query_coverage_threshold: 90 wf|selector: bypass_nucleotide_index g_p_quant|gap_fill: True g_p_quant|minpath: True g_p_quant|pathways: metacyc g_p_quant|xipe: False g_p_quant|annotation_gene_index: 3 out|output_basename: humann out|output_format: tsv out|output_max_decimals: 10 out|remove_column_description_output: False out|intermediate_temp: |
name: value name: value name: value name: value |
demo.sam value |
| Test-5 |
in|input: demo.fastq.gz in|selector: raw wf|translated_search|protein_db|protein_database: uniref-DEMO_diamond-20210421 wf|translated_search|protein_db|selector: cached wf|translated_search|evalue: 1 wf|translated_search|translated_subject_coverage_threshold: 50 wf|translated_search|translated_query_coverage_threshold: 90 wf|selector: bypass_nucleotide_search g_p_quant|gap_fill: True g_p_quant|minpath: True g_p_quant|pathways: metacyc g_p_quant|xipe: False g_p_quant|annotation_gene_index: 3 out|output_basename: humann out|output_format: tsv out|output_max_decimals: 10 out|remove_column_description_output: False out|intermediate_temp: |
name: value name: value name: value name: value |
demo.fastq.gz value |
| Test-6 |
in|input: demo.fastq.gz in|selector: raw wf|prescreen|metaphlan_db|cached_db: metaphlan-demo-db-20210421 wf|prescreen|metaphlan_db|selector: cached wf|prescreen|prescreen_threshold: 0.01 wf|nucleotide_search|nucleotide_db|nucleotide_database: chocophlan-DEMO-20210421 wf|nucleotide_search|nucleotide_db|selector: cached wf|nucleotide_search|nucleotide_identity_threshold: 0 wf|nucleotide_search|nucleotide_subject_coverage_threshold: 50 wf|nucleotide_search|nucleotide_query_coverage_threshold: 90 wf|selector: bypass_translated_search g_p_quant|gap_fill: True g_p_quant|minpath: True g_p_quant|pathways: metacyc g_p_quant|xipe: False g_p_quant|annotation_gene_index: 3 out|output_basename: newname out|output_format: tsv out|output_max_decimals: 10 out|remove_column_description_output: False out|intermediate_temp: |
name: value name: value name: value name: value |
demo.fastq.gz value |