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Revision: 15:eca2e2e20436

Repository 'metaphlan'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/metaphlan

MetaPhlAn tool metadata

Miscellaneous

Name: MetaPhlAn

Description: to profile the composition of microbial communities

Id: metaphlan

Guid: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4

Version: 4.1.1+galaxy4

Version command string: metaphlan -v

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.2.4+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy3

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy2

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy3

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy2

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.5+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.3+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/3.0.14+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/3.0.13+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/3.0.9+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/3.0.8+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/3.0.7+galaxy0

metaphlan

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

metaphlan

4.1.1

package

Functional tests

name

inputs

outputs

required files

Test-1

inputs|in|raw_in|in: no_taxon_input.fasta
inputs|in|raw_in|selector: single
inputs|in|read_min_len: 70
inputs|in|mapping|bt2_ps: sensitive
inputs|in|mapping|min_mapq_val: 5
inputs|in|selector: raw
inputs|db|cached_db: test-db-20210409
inputs|db|db_selector: cached
analysis|analysis_type|tax_lev|split_levels: True
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|avoid_disqm: True
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: False
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: True

name: value
name: value
name: value
name: value
name: value

no_taxon_input.fasta
value

Test-2

inputs|in|raw_in|in: SRS014464-Anterior_nares.fasta.gz
inputs|in|raw_in|selector: single
inputs|in|read_min_len: 70
inputs|in|mapping|bt2_ps: sensitive
inputs|in|mapping|min_mapq_val: 5
inputs|in|selector: raw
inputs|db|cached_db: test-db-20210409
inputs|db|db_selector: cached
analysis|analysis_type|tax_lev|split_levels: True
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|avoid_disqm: True
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: False
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: True

name: value
name: value
name: value
name: value
name: value

SRS014464-Anterior_nares.fasta.gz
value

Test-3

inputs|in|raw_in|in: ['SRS014464-Anterior_nares.fasta.gz', 'SRS014464-Anterior_nares.fasta.gz']
inputs|in|raw_in|selector: multiple
inputs|in|read_min_len: 70
inputs|in|mapping|bt2_ps: sensitive
inputs|in|mapping|min_mapq_val: 5
inputs|in|selector: raw
inputs|db|bowtie2db: test-db.fasta
inputs|db|mpa_pkl: test-db.json
inputs|db|db_selector: history
analysis|analysis_type|tax_lev|split_levels: False
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|avoid_disqm: True
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: False
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: False

name: value
name: value
name: value
name: value

SRS014464-Anterior_nares.fasta.gz
test-db.fasta
test-db.json
value

Test-4

inputs|in|raw_in|in_f: SRS014464-Anterior_nares.fastq.gz
inputs|in|raw_in|in_r: SRS014464-Anterior_nares.fastq.gz
inputs|in|raw_in|selector: paired
inputs|in|read_min_len: 70
inputs|in|mapping|bt2_ps: sensitive
inputs|in|mapping|min_mapq_val: 5
inputs|in|selector: raw
inputs|db|cached_db: test-db-20210409
inputs|db|db_selector: cached
analysis|analysis_type|tax_lev|split_levels: False
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|avoid_disqm: True
subsample|subsampling_paired: 20257
subsample|subsampling_seed: 42
subsample|selector: paired
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: False
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: False

name: value
name: value
name: value
name: value

SRS014464-Anterior_nares.fastq.gz
value

Test-5

inputs|in|raw_in|in: paired collection
inputs|in|raw_in|selector: paired_collection
inputs|in|read_min_len: 70
inputs|in|mapping|bt2_ps: sensitive
inputs|in|mapping|min_mapq_val: 5
inputs|in|selector: raw
inputs|db|cached_db: test-db-20210409
inputs|db|db_selector: cached
analysis|analysis_type|tax_lev|split_levels: False
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|avoid_disqm: True
subsample|subsampling_paired: 20257
subsample|subsampling_seed: 42
subsample|selector: paired
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: False
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: False

name: value
name: value
name: value
name: value

SRS014464-Anterior_nares.fastq.gz
value

Test-6

inputs|in|raw_in|in: paired collection
inputs|in|raw_in|selector: paired_collection
inputs|in|read_min_len: 70
inputs|in|mapping|bt2_ps: sensitive
inputs|in|mapping|min_mapq_val: 5
inputs|in|selector: raw
inputs|db|cached_db: test-db-20210409
inputs|db|db_selector: cached
analysis|analysis_type|tax_lev|split_levels: False
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|avoid_disqm: True
subsample|selector: no
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: False
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: False

name: value
name: value
name: value
name: value

SRS014464-Anterior_nares_mini.fastq
value

Test-7

inputs|in|in: SRS014464-Anterior_nares.sam
inputs|in|selector: sam
inputs|db|cached_db: test-db-20210409
inputs|db|db_selector: cached
analysis|analysis_type|tax_lev|split_levels: False
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|avoid_disqm: True
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: False
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: False

name: value
name: value

SRS014464-Anterior_nares.sam
value

Test-8

inputs|in|in: SRS014464-Anterior_nares-bowtie2out.tabular
inputs|in|selector: bowtie2out
inputs|db|cached_db: test-db-20210409
inputs|db|db_selector: cached
analysis|analysis_type|tax_lev|split_levels: False
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|avoid_disqm: True
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: False
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: False

name: value
name: value

SRS014464-Anterior_nares-bowtie2out.tabular
value

Test-9

inputs|in|raw_in|in: SRS014464-Anterior_nares.fasta
inputs|in|raw_in|selector: single
inputs|in|read_min_len: 70
inputs|in|mapping|bt2_ps: sensitive
inputs|in|mapping|min_mapq_val: 5
inputs|in|selector: raw
inputs|db|cached_db: test-db-20210409
inputs|db|db_selector: cached
analysis|analysis_type|tax_lev|split_levels: True
analysis|analysis_type|tax_lev|tax_lev: a
analysis|analysis_type|t: rel_ab
analysis|min_cu_len: 2000
analysis|organism_profiling: add_viruses
analysis|stat: avg_g
analysis|stat_q: 0.2
analysis|perc_nonzero: 0.33
analysis|ignore_markers: marker.txt
analysis|avoid_disqm: True
out|sample_id_key: SampleID
out|sample_id: Metaphlan_Analysis
out|use_group_representative: False
out|legacy_output: True
out|CAMI_format_output: False
out|unclassified_estimation: False
out|krona_output: True

name: value
name: value
name: value
name: value
name: value

SRS014464-Anterior_nares.fasta
marker.txt
value

Test-10

inputs|in|raw_in|in: SRS014464-Anterior_nares.fastq.gz
inputs|in|raw_in|selector: single
inputs|in|selector: raw
inputs|db|cached_db: mpa_vJan21_TOY_CHOCOPhlAnSGB
inputs|db|db_selector: cached
analysis|analysis_type|t: marker_ab_table
subsample|subsampling: 10000
subsample|subsampling_seed: 42
subsample|selector: single
viral_analysis|profile_vsc: --profile_vsc
test: true

name: value
name: value
name: value

SRS014464-Anterior_nares.fastq.gz
value