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This section contains detailed description of all workflow elements presented in the Workflow Designer.

For each element you can find:

  • Description of the parameters used in the GUI
  • Corresponding parameters names used in a workflow file
  • Information about input and output ports

The type of a parameter can be one of the following:

string

A string.

numeric

A number.

boolean

A boolean data type. Available values are: true / false, 0 / 1 and yes / no.

A port’s slot type can be one of the following:

sequence

Biological sequence

msa

Multiple sequence alignment

text

A text

annotation-table

Table of annotations

annotation-table-list

A list of different tables of annotations

ebwt-index

 Bowtie index

hmm2-profile

A HMM profile of HMMER2 package

fmatrix

 Frequency matrix

wmatrix

Weight matrix

sitecon-model

 SITECON model

assembly

Assembly

variation

Variation track

To search an element use the name filter or press the Ctrl+F shortcut that moves you to the name filter also:

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