Workflow Designer Documentation v. 33
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  • Filter by Classification
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The filter takes files with NGS reads or contigs, classified by one of the tools: Kraken, CLARK, DIAMOND, WEVOTE.

For each input file, it outputs a file with unspecific sequences (i.e. sequences not classified by the tools, taxID = 0) and/or one or several files with sequences that belong to the specific taxonomic group(s).

Parameters in GUI

 

ParameterDescriptionDefaultvalue
Input data

To filter single-end (SE) reads or contigs, received by reads de novo assembly, set this parameter to "SE reads or contigs". Use the "Input URL 1" slot of the input port.
To filter paired-end (PE) reads, set the value to "PE reads". Use the ""Input URL 1" and "Input URL 2" slots of the input port to input the NGS reads data.
Also, input the classification data, received from Kraken, CLARK, or DIAMOND, to the "Taxonomy classification data" input slot.
Either one or two slots of the output port are used depending on the input data.

SE reads or contigs
Save unspecific sequences

Select "True" to put all unspecific input sequences (i. e. sequences with tax ID = 0) into a separate file.
Select "False" to skip unspecific sequences. At least one specific taxon should be selected in the "Save sequences with taxID" parameter in this case.

True

Save sequences with taxIDSelect a taxID to put all sequences that belong to this taxonomic group (i. e. the specified taxID and all children in the taxonomy tree) into a separate file. 

Parameters in Workflow File

Type: classification-filter

Parameter

Parameter in the GUI

Type

sequencing-reads

Input data

string

save-unspecific-sequences

Save unspecific sequences

bool

tax-ids

Save sequences with taxIDstring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequences and tax IDs: 

The following input should be provided:

  • URL(s) to FASTQ or FASTA file(s).
  • Corresponding taxonomy classification of sequences in the files.

To process single-end reads or contigs, pass the URL(s) to the "Input URL 1" slot.

To process paired-end reads, pass the URL(s) to files with the "left" and "right" reads to the "Input URL 1" and "Input URL 2" slots correspondingly.

The taxonomy classification data are received by one of the classification tools (Kraken, CLARK, or DIAMOND) and should correspond to the input files.

Name in Workflow File: in

Slots:

SlotInGUISlot in Workflow FileType
Input URLurlstring

 

Taxonomy datatax-data

tax-classification 

The element has 1 output port:

Name in GUI: Output file(s):  

 

The port outputs URLs to files with NGS reads, classified by taxon IDs: one file per each specified taxon ID per each input file (or the pair of files in case of PE reads).

Either one (for SE reads or contigs) or two (for PE reads) output slots are used depending on the input data. See also the "Input data" parameter of the element.

Name in Workflow File: out

Slots:

SlotInGUISlot in Workflow FileType
Output URL 1

url

string

Output URL 2urlstring
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