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taverna filter

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taverna


Runs workflows in Taverna via command line tool.

Aliases for this filter

  • taverna

Converts from file formats:

  • .t2flow

To file formats:

  • .txt

Available settings:

SettingDescriptionDefault
add-new-filesBoolean or list of extensions/patterns to match.True
added-in-versionDexy version when this filter was first available.
additional-doc-filtersFilters to apply to additional documents created as side effects.{}
additional-doc-settingsSettings to apply to additional documents created as side effects.{}
argsArguments to be passed to the executable.
check-return-codeWhether to look for nonzero return code.True
clargsArguments to be passed to the executable (same as 'args').
command-stringThe full command string.%(prog)s %(args)s "%(script_file)s" %(scriptargs)s
data-typeAlias of custom data class to use to store filter output.generic
envDictionary of key-value pairs to be added to environment for runs.{}
examplesTemplates which should be used as examples for this filter.[]
exclude-add-new-filesList of patterns to skip even if they match add-new-files.[]
exclude-new-files-from-dirList of directories to skip when adding new files.[]
executableThe executable to be runtaverna
extFile extension to output.None
extension-mapDictionary mapping input extensions to default output extensions.None
helpHelpstring for plugin.Runs workflows in Taverna via command line tool.
initial-timeout10
input-extensionsList of extensions which this filter can accept as input.['.t2flow']
keep-originalsWhether, if additional-doc-filters are specified, the original unmodified docs should also be added.False
make-dummy-outputWhether to make a dummy output file when one is not generated and add-new-files is True.False
mkdirA directory which should be created in working dir.None
mkdirsA list of directories which should be created in working dir.[]
nodocWhether filter should be excluded from documentation.False
outputWhether to output results of this filter by default by reporters such as 'output' or 'website'.False
output-extensionsList of extensions which this filter can produce as output.['.txt']
override-workspace-exclude-filtersIf True, document will be populated to other workspaces ignoring workspace-exclude-filters.False
path-extensionsstrings to extend path with[]
preserve-prior-data-classWhether output data class should be set to match the input data class.False
record-varsWhether to add code that will automatically record values of variables.False
require-outputShould dexy raise an exception if no output is produced by this filter?False
scriptargsArguments to be passed to the executable.
tagsTags which describe the filter.['repro', 'workflow']
taverna-homeLocation of taverna home directory.$TAVERNA_HOME
timeout10
use-wdWhether to use a custom working directory when running filter.True
variablesA dictionary of variable names and values to make available to this filter.{}
varsA dictionary of variable names and values to make available to this filter.{}
version-commandCommand to call to return version of installed software.None
windows-version-commandCommand to call on windows to return version of installed software.None
workspace-exclude-filtersFilters whose output should be excluded from workspace.['pyg']
workspace-includesIf set to a list of filenames or extensions, only these will be populated to working dir.None
write-stderr-to-stdoutShould stderr be piped to stdout?False
x-maxJava -Xmx setting300m
x-perm-maxJava -XX:MaxPermSize setting140m
Filter Source Code
class Taverna(SubprocessStdoutFilter):
    """
    Runs workflows in Taverna via command line tool.
    """
    aliases = ['taverna']
    _settings = {
            'executable' : 'taverna',
            'tags' : ['repro', 'workflow'],
            'add-new-files' : True,
            'input-extensions' : ['.t2flow'],
            'output-extensions' : ['.txt'],
            'taverna-home' : ("Location of taverna home directory.", "$TAVERNA_HOME"),
            'x-max' : ("Java -Xmx setting", '300m'),
            'x-perm-max' : ("Java -XX:MaxPermSize setting", '140m'),
            }

    def command_string(self):
        assert self.setting('taverna-home')

        return """java -Xmx%(x-max)s -XX:MaxPermSize=%(x-perm-max)s \\
                -Draven.profile=file://%(taverna-home)s/conf/current-profile.xml \\
                -Dtaverna.startup=%(taverna-home)s \\
                -Djava.system.class.loader=net.sf.taverna.raven.prelauncher.BootstrapClassLoader \\
                -Draven.launcher.app.main=net.sf.taverna.t2.commandline.CommandLineLauncher \\
                -Draven.launcher.show_splashscreen=false \\
                -Djava.awt.headless=true \\
                -jar "%(taverna-home)s/lib/"prelauncher-*.jar \\
                %(script_file)s""" % self.command_string_args()

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