taverna-commandline-common/src/main/resources/help.txt

By default, the workflow is executed using the -inmemory option, and the
results are written out to a directory named after the workflow name.

If this directory already exists then a new directory is created, and
appended with _<n>, where n is incremented to the next available index.

Results are written out 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.

You can also record your results to a Baclava document using -outputdoc
option. The document will be overwritten if it already exists.

Inputs can be provided in three ways. Both -inputfile and -inputvalue options
can be used together; -inputdoc option must be used on its own. -inputfile and
-inputvalue options 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. ;.

If a list of greater depth (i.e. a list or lists or deeper) is required then
you will need to use the -inputdoc option.  However, if you provide an input
of lower depth to that required, then it will automatically be wrapped in one
or more lists up to the required depth. Providing an input of greater depth
than that required will result in an error.

If a workflow has a high memory requirement, then it may be better to run it
using a database to store data rather than storing it in memory, which is the
default option. There are three options for using a database:

-embedded option, runs with an embedded database. This is slightly faster than
the -clientserver option (below), but has the limitation that only one
executeworkflow script may be executed simultaneously.

-clientserver option allows the workflow to be executed backed by the database
running as a server. By default a database is not started for you, but may be
started using -startdb option.

-startdb option starts a database. It may be used without providing a workflow
to allow a database to be started separately, allowing multiple simultaneous
executeworkflow script runs.

More advanced database configurations can be specified using -dbproperties
option, allowing you to take full control over the database used. This takes a
second argument, the filename of the properties file, for which the following
example contains the default settings:

in_memory = true
provenance = false
connector = derby
port = 1527
dialect = org.hibernate.dialect.DerbyDialect
start_derby = false
driver = org.apache.derby.jdbc.EmbeddedDriver
jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true

Note that when using -dbproperties together with other options, the other
options take precedence.

-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 (depending on the platform).

-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.