MetaPhlAn2 (METAgenomic PHyLogenetic ANalysis) is a tool for profiling the composition of microbial communities (bacteria, archaea, eukaryotes, and viruses) from whole-metagenome shotgun sequencing data.
Parameters in GUI
Parameter | Description | Defaultvalue |
---|---|---|
Input data | To classify single-end (SE) reads or contigs, received by reads de novo assembly, set this parameter to "SE reads or contigs". | SE reads or contigs |
Input file format | Set type of an input file (--input-type). Each input file will usually contain a lot of sequences that should be classified. | FASTA
|
Database | A path to a folder with MetaPhlAn2 database: BowTie2 index files, built from reference genomes, and *.pkl file (--mpa-pkl, --bowtie2db). | |
Number of threads | The number of CPUs to use for parallelizing the mapping (--nproc). | 8 |
Analysis type | Specify the type of analysis to perform:
| Relative abundance |
Tax level | The taxonomic level for the relative abundance output: all, kingdoms (Bacteria and Archaea) only, phyla only, etc. (--tax_lev). | All |
Bowtie2 output file | The file for saving the output of BowTie2 (--bowtie2out). In case of PE reads one file is created per each pair of files. | Auto |
Output file | MetaPhlAn2 output depends on the "Analysis type" parameter. By default, it is a tab-delimited file with the predicted taxon relative abundances. | Auto |
Parameters in Workflow File
Type: metaphlan2-classify
Parameter | Parameter in the GUI | Type |
---|---|---|
input-data | Input data | string |
input-format | Input file format | string |
database | Database | string |
threads | Number of threads | number |
analysis-type | Analysis type | string |
tax-level | Tax level | string |
bowtie2-output-url | Bowtie2 output file | string |
output-url | Output file | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input sequences:
URL(s) to FASTQ or FASTA file(s) should be provided. In case of SE reads or contigs use the "Input URL 1" slot only. In case of PE reads input "left" reads to "Input URL 1", "right" reads to "Input URL 2".See also the "Input data" parameter of the element
Name in Workflow File: in
Slots:
SlotInGUI | Slot in Workflow File | Type |
---|---|---|
Input URL | url | string |