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.
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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.
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The item becomes invisible, but its value is sent to a command line if that property is active.
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Property name can be changed using "Property Rename" command from contextual menu.
To define program input, two subsections: XX.Option and XX.Input shall be filled.
means that file exists,
- path to file is wrong or file does not exist.
button) is used as an input. In such case MolQuest runs several passes, one file from a list at a time,
in the same order they appear in a dialog window, until all files are processed. Results of each
pass are shown in a list in Results Tab.
Icon
indicates that file list is empty, while
means that it is not.
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In File List dialog (see picture below), pressing
button opens standard Add File window, which is used to add files to a list.
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Order of files in a list can be changed by using
and
buttons.
To remove an individual file from a list, press
button, and to remove all files,
button.
,while undefined or wrong link - by icon
. Similarly,
icon means that destination for output data is correct, and
the 
-
that link is not defined or incorrect.
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.
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To define an output file, two subsections: XX.Option and XX.Output should be filled.
icon means that output
means that output data destination is correct,
the
that link is not defined or wrong.
icon means that output
means that output data destination is correct,
the
that link is not defined or wrong.
If STDOUT subsections are not set, but a program outputs data to standard output, it would generate a warning.
icon means that output
means that output data destination is correct,
the
that link is not defined or wrong.
If STDERR subsections are not set, but a program outputs data there, it would generate a warning.
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.