Skip to end of metadata
Go to start of metadata

The command tab is where you specify the commands that will be run for the tool service.

Type the commands that you want to run into the text area.

You only need to make changes to the commands when you want part of them to be replaced by strings input into the tool service when it is executed. In this case %%first_name%% and %%second_name%% will be replaced by data when the tool service is executed.

When you use SSH to access a machine, you may not have the same PATH as when you log into the machine. As a result, the commands may not be readily available. You need to either check the PATH you get via SSH or use explicit paths to the commands.

If you are writing data to a file, then you do not need to put %% round the name of the file.

The commands will be executed either as a stand-alone process or within a shell. You can change how this happens as part of the invocation location.

When the calling of the commands has finished, they will return a status code. By default, Taverna treats any non-zero return code as indicating that the tool has failed. If you want to add more acceptable return codes, then you can specify a comma-separated list of return codes in Valid return codes.

The tool service allows you to pass data into the standard input stream (STDIN) of the tool service, and to read data from the standard output (STDOUT) and error (STDERR) streams. These streams are shown as input and output ports of the tool service. By default, the tool service shows the STDOUT and STDERR but not the STDIN. You can use the Show STDIN, Show STDOUT and Show STDERR tick boxes to change this.

In addition to being able to read tool descriptions from a registry, you can also read a description from a file. When you click on the Load description button, you can select a file that contains descriptions. If that file contains more than one description, then you can select which description to read. The whole of the tool service description will be replaced by the description read from the file.

Similarly, you can save your tool description to a file by clicking on the Export description button. The file can contain several descriptions and Taverna will overwrite any existing description of the same name in the file. Before you are able to save a tool description, Taverna will check that you have entered the necessary annotation information.

Pressing the Clear script button will clear the set of commands shown in this tab. It has no effect on the content of the other tabs.

Labels
  • None