Repository revision
6:c2803012bbb3

Repository 'humann'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/humann

HUMAnN tool metadata
Miscellaneous
HUMAnN
to profile presence/absence and abundance of microbial pathways and gene families
humann
toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0
3.9+galaxy0
humann --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.7+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.6.1+galaxy0
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
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 3.9 package
Additional information about this tool
#import re
#if $in.input.ext.startswith("fasta")
    #set ext="fasta"
#else if $in.input.ext.startswith("fastq")
    #set ext="fastq"
#else if $in.input.ext.endswith("bam")
    #set ext="bam"
#else if $in.input.ext == 'sam'
    #set ext="sam"
#else if $in.input.ext == 'biom1'
    #set ext="biom"
#else
    >&2 "unknown extension $in.input.ext"
    exit 1; 
#end if
#if $in.input.ext.endswith(".gz")
    #set ext+=".gz"
#end if

#if $wf.selector == 'bypass_prescreen'
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            mkdir nucleotide_db
            &&
                #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database:
            ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v201901_v31' &&
                #end for
            #end if
        
    
            #if $wf.translated_search.protein_db.selector == 'history'
            mkdir protein_db
            &&
            diamond makedb
                --in '$wf.translated_search.protein_db.protein_database'
                --db 'protein_db/protein-db-201901b'
                --threads "\${GALAXY_SLOTS:-4}"
            &&
            #end if
        
#else if $wf.selector == 'bypass_taxonomic_profiling'
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            mkdir nucleotide_db
            &&
                #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database:
            ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v201901_v31' &&
                #end for
            #end if
        
    
            #if $wf.translated_search.protein_db.selector == 'history'
            mkdir protein_db
            &&
            diamond makedb
                --in '$wf.translated_search.protein_db.protein_database'
                --db 'protein_db/protein-db-201901b'
                --threads "\${GALAXY_SLOTS:-4}"
            &&
            #end if
        
#else if $wf.selector == 'bypass_nucleotide_index'
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            mkdir nucleotide_db
            &&
                #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database:
            ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v201901_v31' &&
                #end for
            #end if
        
    
            #if $wf.translated_search.protein_db.selector == 'history'
            mkdir protein_db
            &&
            diamond makedb
                --in '$wf.translated_search.protein_db.protein_database'
                --db 'protein_db/protein-db-201901b'
                --threads "\${GALAXY_SLOTS:-4}"
            &&
            #end if
        
#else if $wf.selector == 'bypass_nucleotide_search'
    
            #if $wf.translated_search.protein_db.selector == 'history'
            mkdir protein_db
            &&
            diamond makedb
                --in '$wf.translated_search.protein_db.protein_database'
                --db 'protein_db/protein-db-201901b'
                --threads "\${GALAXY_SLOTS:-4}"
            &&
            #end if
        
#else if $wf.selector == 'bypass_translated_search'
    
            #if $wf.prescreen.metaphlan_db.selector == "history"
            mkdir metaphlan_db
            &&
            bowtie2-build --large-index '$wf.prescreen.metaphlan_db.bowtie2db' 'metaphlan_db/custom_db-v30'
            &&
            python '$__tool_directory__/customizemetadata.py'
                transform_json_to_pkl
                --json '$wf.prescreen.metaphlan_db.mpa_pkl'
                --pkl 'metaphlan_db/custom_db-v30.pkl'
            &&
            #end if
        
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            mkdir nucleotide_db
            &&
                #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database:
            ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v201901_v31' &&
                #end for
            #end if
        
#else if $wf.selector == 'none'
    
            #if $wf.prescreen.metaphlan_db.selector == "history"
            mkdir metaphlan_db
            &&
            bowtie2-build --large-index '$wf.prescreen.metaphlan_db.bowtie2db' 'metaphlan_db/custom_db-v30'
            &&
            python '$__tool_directory__/customizemetadata.py'
                transform_json_to_pkl
                --json '$wf.prescreen.metaphlan_db.mpa_pkl'
                --pkl 'metaphlan_db/custom_db-v30.pkl'
            &&
            #end if
        
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            mkdir nucleotide_db
            &&
                #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database:
            ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v201901_v31' &&
                #end for
            #end if
        
    
            #if $wf.translated_search.protein_db.selector == 'history'
            mkdir protein_db
            &&
            diamond makedb
                --in '$wf.translated_search.protein_db.protein_database'
                --db 'protein_db/protein-db-201901b'
                --threads "\${GALAXY_SLOTS:-4}"
            &&
            #end if
        
#end if

humann
    --input '$input'
    --input-format $ext
    -o 'output'
#if $wf.selector == 'bypass_prescreen'
    --bypass-prescreen
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            --nucleotide-database nucleotide_db
            #else
            --nucleotide-database '$wf.nucleotide_search.nucleotide_db.nucleotide_database.fields.path'
            #end if
            --nucleotide-identity-threshold $wf.nucleotide_search.nucleotide_identity_threshold
            --nucleotide-subject-coverage-threshold $wf.nucleotide_search.nucleotide_subject_coverage_threshold
            --nucleotide-query-coverage-threshold $wf.nucleotide_search.nucleotide_query_coverage_threshold
            
    
            --translated-alignment 'diamond'
            #if $wf.translated_search.protein_db.selector == 'history'
            --protein-database protein_db
            --search-mode '$wf.translated_search.protein_db.search_mode'
            #else
            --protein-database '$wf.translated_search.protein_db.protein_database.fields.path'
                #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.value
            --search-mode 'uniref50'
                #else
            --search-mode 'uniref90'
                #end if
            #end if
            --evalue $wf.translated_search.evalue
            #if str($wf.translated_search.translated_identity_threshold) != ''
            --identity-threshold $wf.translated_search.translated_identity_threshold
            #end if
            --translated-subject-coverage-threshold $wf.translated_search.translated_subject_coverage_threshold
            --translated-query-coverage-threshold $wf.translated_search.translated_query_coverage_threshold
        
#else if $wf.selector == 'bypass_taxonomic_profiling'
    --taxonomic-profile '$wf.taxonomic_profile'
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            --nucleotide-database nucleotide_db
            #else
            --nucleotide-database '$wf.nucleotide_search.nucleotide_db.nucleotide_database.fields.path'
            #end if
            --nucleotide-identity-threshold $wf.nucleotide_search.nucleotide_identity_threshold
            --nucleotide-subject-coverage-threshold $wf.nucleotide_search.nucleotide_subject_coverage_threshold
            --nucleotide-query-coverage-threshold $wf.nucleotide_search.nucleotide_query_coverage_threshold
            
    
            --translated-alignment 'diamond'
            #if $wf.translated_search.protein_db.selector == 'history'
            --protein-database protein_db
            --search-mode '$wf.translated_search.protein_db.search_mode'
            #else
            --protein-database '$wf.translated_search.protein_db.protein_database.fields.path'
                #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.value
            --search-mode 'uniref50'
                #else
            --search-mode 'uniref90'
                #end if
            #end if
            --evalue $wf.translated_search.evalue
            #if str($wf.translated_search.translated_identity_threshold) != ''
            --identity-threshold $wf.translated_search.translated_identity_threshold
            #end if
            --translated-subject-coverage-threshold $wf.translated_search.translated_subject_coverage_threshold
            --translated-query-coverage-threshold $wf.translated_search.translated_query_coverage_threshold
        
#else if $wf.selector == 'bypass_nucleotide_index'
    --bypass-nucleotide-index
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            --nucleotide-database nucleotide_db
            #else
            --nucleotide-database '$wf.nucleotide_search.nucleotide_db.nucleotide_database.fields.path'
            #end if
            --nucleotide-identity-threshold $wf.nucleotide_search.nucleotide_identity_threshold
            --nucleotide-subject-coverage-threshold $wf.nucleotide_search.nucleotide_subject_coverage_threshold
            --nucleotide-query-coverage-threshold $wf.nucleotide_search.nucleotide_query_coverage_threshold
            
    
            --translated-alignment 'diamond'
            #if $wf.translated_search.protein_db.selector == 'history'
            --protein-database protein_db
            --search-mode '$wf.translated_search.protein_db.search_mode'
            #else
            --protein-database '$wf.translated_search.protein_db.protein_database.fields.path'
                #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.value
            --search-mode 'uniref50'
                #else
            --search-mode 'uniref90'
                #end if
            #end if
            --evalue $wf.translated_search.evalue
            #if str($wf.translated_search.translated_identity_threshold) != ''
            --identity-threshold $wf.translated_search.translated_identity_threshold
            #end if
            --translated-subject-coverage-threshold $wf.translated_search.translated_subject_coverage_threshold
            --translated-query-coverage-threshold $wf.translated_search.translated_query_coverage_threshold
        
#else if $wf.selector == 'bypass_nucleotide_search'
    --bypass-nucleotide-search
    
            --translated-alignment 'diamond'
            #if $wf.translated_search.protein_db.selector == 'history'
            --protein-database protein_db
            --search-mode '$wf.translated_search.protein_db.search_mode'
            #else
            --protein-database '$wf.translated_search.protein_db.protein_database.fields.path'
                #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.value
            --search-mode 'uniref50'
                #else
            --search-mode 'uniref90'
                #end if
            #end if
            --evalue $wf.translated_search.evalue
            #if str($wf.translated_search.translated_identity_threshold) != ''
            --identity-threshold $wf.translated_search.translated_identity_threshold
            #end if
            --translated-subject-coverage-threshold $wf.translated_search.translated_subject_coverage_threshold
            --translated-query-coverage-threshold $wf.translated_search.translated_query_coverage_threshold
        
#else if $wf.selector == 'bypass_translated_search'
    --bypass-translated-search
    
            #set $metaphlan_option = "-t rel_ab"
            #if $wf.prescreen.metaphlan_db.selector == "history"
                #set $metaphlan_option += " --bowtie2db metaphlan_db/"
                #set $metaphlan_option += " --index custom_db-v30"
            #else
                #set $metaphlan_option += " --bowtie2db %s" % $wf.prescreen.metaphlan_db.cached_db.fields.path
                #set $metaphlan_option += " --index %s" % $wf.prescreen.metaphlan_db.cached_db.fields.dbkey
            #end if
            --metaphlan-options="$metaphlan_option"
            --prescreen-threshold $wf.prescreen.prescreen_threshold
        
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            --nucleotide-database nucleotide_db
            #else
            --nucleotide-database '$wf.nucleotide_search.nucleotide_db.nucleotide_database.fields.path'
            #end if
            --nucleotide-identity-threshold $wf.nucleotide_search.nucleotide_identity_threshold
            --nucleotide-subject-coverage-threshold $wf.nucleotide_search.nucleotide_subject_coverage_threshold
            --nucleotide-query-coverage-threshold $wf.nucleotide_search.nucleotide_query_coverage_threshold
            
#else if $wf.selector == 'none'
    
            #set $metaphlan_option = "-t rel_ab"
            #if $wf.prescreen.metaphlan_db.selector == "history"
                #set $metaphlan_option += " --bowtie2db metaphlan_db/"
                #set $metaphlan_option += " --index custom_db-v30"
            #else
                #set $metaphlan_option += " --bowtie2db %s" % $wf.prescreen.metaphlan_db.cached_db.fields.path
                #set $metaphlan_option += " --index %s" % $wf.prescreen.metaphlan_db.cached_db.fields.dbkey
            #end if
            --metaphlan-options="$metaphlan_option"
            --prescreen-threshold $wf.prescreen.prescreen_threshold
        
    
            #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
            --nucleotide-database nucleotide_db
            #else
            --nucleotide-database '$wf.nucleotide_search.nucleotide_db.nucleotide_database.fields.path'
            #end if
            --nucleotide-identity-threshold $wf.nucleotide_search.nucleotide_identity_threshold
            --nucleotide-subject-coverage-threshold $wf.nucleotide_search.nucleotide_subject_coverage_threshold
            --nucleotide-query-coverage-threshold $wf.nucleotide_search.nucleotide_query_coverage_threshold
            
    
            --translated-alignment 'diamond'
            #if $wf.translated_search.protein_db.selector == 'history'
            --protein-database protein_db
            --search-mode '$wf.translated_search.protein_db.search_mode'
            #else
            --protein-database '$wf.translated_search.protein_db.protein_database.fields.path'
                #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.value
            --search-mode 'uniref50'
                #else
            --search-mode 'uniref90'
                #end if
            #end if
            --evalue $wf.translated_search.evalue
            #if str($wf.translated_search.translated_identity_threshold) != ''
            --identity-threshold $wf.translated_search.translated_identity_threshold
            #end if
            --translated-subject-coverage-threshold $wf.translated_search.translated_subject_coverage_threshold
            --translated-query-coverage-threshold $wf.translated_search.translated_query_coverage_threshold
        
#end if
    --gap-fill '$g_p_quant.gap_fill'
    --minpath '$g_p_quant.minpath'
    --pathways '$g_p_quant.pathways' 
    --xipe '$g_p_quant.xipe'
    --annotation-gene-index $g_p_quant.annotation_gene_index
#if $g_p_quant.id_mapping
    --id-mapping '$g_p_quant.id_mapping'
#end if
    --log-level 'DEBUG'
    --o-log '$log'
    --output-basename '$out.output_basename'
    --output-format '$out.output_format'
    --output-max-decimals $out.output_max_decimals
    $out.remove_column_description_output
    $out.remove_stratified_output
    --threads "\${GALAXY_SLOTS:-4}"
    --memory-use minimum
None
False
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/old-structure/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|selector: none
 demo.fastq.gz
test-db/metaphlan-db/demo-db-v30.fasta
test-db/metaphlan-db/old-structure/demo-db-v30.json
test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz
test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz
Test-2 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.v201901_v31.ffn.gz
test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz
test-db/protein-db/uniref90_demo_prots_v201901b.fasta
value
Test-3 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-4 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-5 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-6 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-7 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
Test-8 in|input: demo.fastq.gz
in|selector: raw
wf|prescreen|metaphlan_db|cached_db: metaphlan-db-old-structure
wf|prescreen|metaphlan_db|selector: cached
wf|nucleotide_search|nucleotide_db|nucleotide_database: chocophlan-DEMO-20210421
wf|nucleotide_search|nucleotide_db|selector: cached
wf|selector: bypass_translated_search
 demo.fastq.gz