| By default, the workflow results are written to a directory |
| named after the workflow name. If this directory already exists, |
| then a new directory is created with an incremental number. |
| |
| Results are written to files named after the output port for that result. |
| If a result is composed of lists, then a directory is created for the output |
| port and individual list items are named after the list element index (with 1 |
| being the first index). The the output is the result of an error, the filename |
| is appended with '.error'. |
| |
| You can provide your own output directory with the -outputdir option. There |
| will be an error if the directory already exists. |
| |
| Inputs can be provided in three ways. Both -inputfile and -inputvalue options |
| can be used together; both take two additional arguments, the name of the port |
| for the input, and either a file containing the input data, or the input value |
| itself respectively. |
| |
| If one of more of your workflow inputs is a list, you can create a list |
| input by using the -inputdelimiter option, which may be used with either |
| -inputfile or -inputvalue. This option takes two parameters - an input name |
| and the delimiter by which to split the input into a list. |
| |
| The delimiter may be a simple character, such as a comma or a new-line |
| character, or a regular expression. The input string, or file, will then be |
| converted into a list being split by the delimiter specified. Make sure to |
| put the delimiter character in quotes as it may be interpreted by the shell |
| as a special character, e.g. ;. |
| |
| -cmdir option lets you specify an absolute path to a directory where |
| Credential Manager's files (keystore and truststore - containing user's |
| credentials and trusted certificates for accessing secure services) are stored. |
| If not specified and the workflow requires access to these files, Taverna will |
| try to find them in the default location in <TAVERNA_HOME>/security somewhere |
| inside user's home directory. |
| |
| -cmpassword option can be used to tell Taverna to expect the password for the |
| Credential Manager on standard input. If the password is not piped in, Taverna |
| will prompt you for it in the terminal and block until it is entered. Do not |
| enter your password in the command line! If -cmpassword option is not specified |
| and -cmdir option is used, Taverna will try to find the password in a special |
| file password.txt in the directory specified with -cmdir option. |
