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• Now you should configure aliases for those parameters and ports and slots that you are going to use from the command line. To do it select the Actions ‣ Configure command line parameter aliases item in the main menu or the Configure command line parameter aliases toolbar button. The following dialog appears:

<center>
  <img src="/wiki/download/attachments/2097213/configure_cmd_aliases_dialogRunning Workflow from the Command Line_1.png"/>
</center>

It contains the list of objects that corresponds to the elements of the workflow. 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): 

<center>
  <img src="/wiki/download/attachments/2097213/in_aliasRunning Workflow from the Command Line_2.png"/>
</center>

And alias out to parameter Output file (of the Write Stockholm element). 

<center>
  <img src="/wiki/download/attachments/2097213/out_aliasRunning Workflow from the Command Line_3.png"/>
</center>

To select ports and slots aliases use the following dialog by the Actions->Configure port and slot aliases main menu item: 

<center>
  <img src="/wiki/download/attachments/2097213/Running Workflow from the Command Line_4.png"/>
</center>

Press the Ok button to save aliases and close the dialog. When you create aliases you can import workflow to element by the Actions->Import workflow to element main menu item.

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

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