Page History

To create an element for a command line tool select either Actions ‣ Create element with command line external tool in the main menu or the following icon on the toolbar: 

<center> 
	<br>
	<img src="/wiki/download/attachments/2097199/external_cmd_tool.png"/> 
	<br>
</center> 

The Configure Element with External Tool wizard appears. On the first page of the wizard input a name and external command-line tool. Letters, numbers and underscores are allowed in the name. 

<center>
  <br>
  <img src="/wiki/download/attachments/24740125/Creating Element_0.jpg"/>
  <br> 
</center>

On the second page add the required input data:

<center>
  <br>
  <img src="/wiki/download/attachments/2097199/external_cmd_tool.png24740125/Creating Element.jpg"/>
  <br> 
</center> 

The Create Element with Command Line Tool wizard appears. On the first third page of the wizard input a name and a description of the element in the Property Editor. Letters, numbers and underscores are allowed in the nameyou can add parameters for the command line tool. Later you would be able to set values for the parameters in the Property Editor.

<center>
  <br>
  <img src="/wiki/download/attachments/209719924740125/Creating Element_1.pngjpg"/>
  <br> 
</center> 

On the second next page add the required input and output data:

<center>
  <br>
  <img src="/wiki/download/attachments/209719924740125/Creating Element_2.pngjpg"/>
  <br> 
</center> 

For each input or output you should:

• Input a name (letters, numbers, and underscores are allowed in the name).
• Select a type: multiple alignment, sequence, sequence with annotations, a set of annotations or string.
• Specify how the input or output should be handled (for example, you can specify that a value of the input parameter should be handled as a FASTA file).
• Optionally input a description.

...

• .

<center> <img src="/wiki/download/attachments/2097199/Creating Element_3.png"/> </center> 

For each attribute For each parameter added you should:

• Input a name (letters, numbers and underscores are allowed in the name).
• Select it’s its type: boolean, number, string or URL.
• Optionally input the description.

On the last next page of the wizard you should input the execution string, i.e. the command that would be executed. 

<center>
  <br>
  <img src="/wiki/download/attachments/1746637724740125/Creating Element_43.pngjpg"/>
  <br> 
</center> 

The signature of the execution string depends on the command that is launched. But the general rule is that input/output data and attributes have prefix $. You can set the parameterized description for the new element (the description that appears not in property editor but on the element itself). In the parameterized description, you also can use parameters substitution with prefix $. If the paths in the execution string contain spaces, they must be enclosed with quotes.

For example? let there be some perl script “myScript.pl” that accepts an input file as the first attribute and accepts the second attribute denoted as “param1”. The command may look as follows:

perl [path_to_script]myScript.pl $infile $param1 > $outfile

Here infile and outfile are input and output data set on the step 2, param1 is an attribute set on the step 3.

On the same wizard page On the next wizard page, you can optionally input the description of the element. It would be shown on the element on the Scene. The description can be parameterized. This means that if you input e.g. an attribute name (with prefix $), the name on the element would be substituted with the value of the corresponding parameter. For example input the following parameters:

<center>
  <br>
  <img src="/wiki/download/attachments/209719924740125/create_elt_cmd_p4_filled.pngCreating Element_4.jpg"/>
  <br> 
</center>

On the next wizard page, you can see the final element summary:

<center>
  <br>
  <img src="/wiki/download/attachments/24740125/Creating Element_5.jpg"/>
  <br> 
</center>

The element created looks as followscreated element is added to the Workflow Designer scene, and can be connected with other elements in a workflow:

<center>
  <br>
  <img src="/wiki/download/attachments/209719924740125/elt_cmd_on_scene.pngCreating Element_6.jpg"/>
  <br>
</center>

The new element also becomes available in the "Custom Elements with External Tools" group on the "Elements" tab of the Workflow Designer palette (at the left part of the window), so that you can use it at any time in other workflow.