[MOBY-guts] biomoby commit
senger@ebi.ac.uk
senger at pub.open-bio.org
Mon Oct 18 14:35:06 UTC 2004
senger
Mon Oct 18 10:35:06 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory pub.open-bio.org:/tmp/cvs-serv2405/src/Clients/help
Modified Files:
MobyGraphs_usage.txt
Log Message:
searching data paths and more, see docs/ChangeLog
moby-live/Java/src/Clients/help MobyGraphs_usage.txt,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2004/09/24 19:52:55 1.4
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2004/10/18 14:35:06 1.5
@@ -1,8 +1,11 @@
Usage:
java MobyGraphs -h[elp]
java MobyGraphs [<find-arguments>] <other-arguments>
+ or
+ run-graphs-client <same arguments as above>
-where <find-arguments> specify what Moby registry to connect to:
+where <find-arguments> specify what Moby registry to connect to (or
+ what cache to use instead):
-e <URL>
<URL> ia an endpoint of a Moby registry
@@ -11,40 +14,109 @@
<namespace> is a URI defining Moby registry's namespace
(default: http://mobycentral.cbr.nrc.ca/MOBY/Central)
+ -cachedir <dir>
+ a directory where to cache information from a Moby registry;
+ depending on -e and -uri there will be a subdirectory in <dir>
+ used; if such subdirectory already exists its contents is used
+ instead fetching data from the Moby registry; if it does not
+ exist it is created and filled with date fetched from the Moby
+ registry
+
where <other-arguments> are:
-
+
+ General arguments:
+ ------------------
-q ... quiet mode
+ graph properties:
+ -rankdir <LR | TB>
+ LR (default): graph directed Left to Right,
+ TB: graph directed Top to Bottom
+
+ Making a graph of data types:
+ -----------------------------
-d ... make graph showing data types
- -s ... make graph showing service instances
+
+ output destination (default: standard output):
+ -fd <file> ... where to put the data types graph
+ -f <file> ... where to put (any) created graph
+
+ Making a graph of service types:
+ --------------------------------
-t ... make graph showing service types
+ output destination (default: standard output):
+ -ft <file> ... where to put the service types graph
+ -f <file> ... where to put (any) created graph
+
+ Making a graph of service instances:
+ ------------------------------------
+ -s ... make graph showing service instances
+
+ output destination (default: standard output):
+ -fs <file> ... where to put the services graph
+ -f <file> ... where to put (any) created graph
+
output format:
- -dot ... (this is default)
- -rdf ... (this works only for graph of services)
+ -dot ... Grapviz 'dot' language (this is default);
+ to display the result use something like:
+ dot -Tpng <file> | display
+ (where <file> is what specified by -f)
+ -rdf ... as RDF (not used for -datapath)
- output filter (what to be included,
- only used for services):
+ output filter (what services to be included):
-auth <authority[,authority]...>
-name <service[,service]...>
-depth <depth> ... an integer, how far to go from
given services (default is 1)
or
-path <service1> <service2>
+ draw all pathes from <service1> to <service2>
- output destinations:
- -fd <file> ... where to put the data types graph
- (makes sense only together with -d)
- -fs <file> ... where to put the services graph
- (makes sense only together with -s)
- -ft <file> ... where to put the service types graph
- (makes sense only together with -t)
- -f <file> ... where to put (any) created graph
- (makes sense only together with -d, -s,
- or -t, but does not make sense if two
- or even all three of them are used)
- default: standard output
+ Making a graph of service instances based on I/O types:
+ -------------------------------------------------------
+ -s ... make graph showing service instances
+
+ -datapath <data-type-name-1> <data-type-name-2>
+ draw path(s) starting in <data-type-name-1> and
+ ending in <data-type-name-2>;
+ <data-type-name-x> can be:
+ namespace/dataTypeName or simply
+ dataTypeName
+ Example: -datapath GO/Object AminoAcidSequence
+
+ -separate ... create one output file for each found path;
+ only paths without cycles and forking are
+ included
+ (this option is automatically implied also when any of
+ arguments -join or -sculf or -onlyscufl are used)
+
+ -join <paths-per-page>
+ create separate paths (as defined by -separate) but
+ join them again together (as parallel graphs) in graphs
+ each of them with maximum <path-per-page> paths
+
+ -scufl ... generate workflow definition (for Taverna)
+ for each separate path
+ -onlyscufl ... do only what -scufl does without generating
+ any graphs
+
+ additional properties for workflow definition
+ (used only with -scufl or -onlyscufl):
+ -rawinput
+ the generated workflow definition will not include input
+ data processors (converting basic data types into Moby XML
+ structure. By default it does.
+ -rawoutput
+ the generated workflow definition will not include output
+ data processors (converting basic data types from Moby XML
+ structure. By default it does.
+ -raw
+ the generated workflow definition will not include input
+ nor output data processors (converting basic data types
+ into/from Moby XML structure. By default it does. This
+ does what -rawinput and -rawoutput do together.
+ -tverbose
+ workflow creation will produce many messages.
+ By default it does not.
- graph properties:
- -rankdir ... values: LR, TB
- default: LR
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