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This chapter describes how you can create a new command using a schemaworkflow.

To run a schema workflow from the command line do the following:

• Create the schema workflow in the Workflow Designer. For example on the image below the Align sequences with MUSCLE sample schema workflow is used:

<center>
  <img src="/wiki/download/attachments/2097213/schema_example.png"/>
</center>

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It contains the list of objects that corresponds to the elements of the schemaworkflow. For each object the list of parameters is available for which you can assign command line aliases. For example, assign alias in to parameter Input file (of the Read alignment element): 

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Press the Ok button to save aliases and close the dialog.

• Save the schemaworkflow to a file: if you follow the example, choose the Actions ‣ Save schema workflow as... item in the main menu, browse for the file location and enter mySchema as the schema workflow name. This name will be used to launch the schema workflow from the command line.
•  Launch the schema workflow from the command line:
  

[path_to_ugene\]ugene --task={schema_name} [--{parameter1}={value1} [--{parameter2}={value2} ...]]

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