User can integrate console applications into MolQuest GUI shell on his own. To do this, add "Standard Template" task from Templates group of Programs list of Toolbox tab. In this template, name and path to an executable file, as well as its running options (input and output files, command line options and other necessary information) have to be specified.

In drop down list at the very top of Properties tab , maximum allowable number of input files (NN Input), output files (NN Outputs) and command line options (NN Options) has to be specified.. For example, "01 Input; 01 Output; 05 Option" means that application can have no more than one input file, one output file and five command line options. Once a program is added, all unused properties can be hidden.

System section

exe section

Common rules for editing the application options:

As for MolQuest's own tasks, "Input files" can be single or multiple files and can be specified by user or taken from a pipeline, and output files can be sent to another task via pipeline.

To activate a property, the appropriate box should be checked ().

To prevent property from being displayed (e.g. a property that doesn't change its value in all conceivable task variants), right-click on it and choose "SubNodes - Permanently Hide" command from contextual menu.

The item becomes invisible, but its value is sent to a command line if that property is active.

Property name can be changed using "Property Rename" command from contextual menu.

Input section

To define program input, two subsections: XX.Option and XX.Input shall be filled.

To choose the link for input data, use button (Placed on In Slots page), which displays "Select Task Output" dialog with list of outputs of task within current project. Moving outputs between "Available pipes" and "Selected pipes" lists is performing by mouse doube-click.

Output section

To define an output file, two subsections: XX.Option and XX.Output should be filled.

If STDOUT subsections are not set, but a program outputs data to standard output, it would generate a warning.

If STDERR subsections are not set, but a program outputs data there, it would generate a warning.

Options section

To define an option, two subsections: XX.Option and XX.Value should be filled.

Once selection is done, all unused subnodes can be hidden. To do so, use "SubNodes Permanently Hide" command from contextual menu.

Once all properties have been specified, the task can be added to repository (Repository tab) for further use in various projects.