[Pipet Devel] command-line composite (was: Attempt at Constructing the Command Line)

[J.W. Bizzaro]

A long time ago, in a galaxy far, far away "J.W. Bizzaro" wrote:
> 
> Brad Chapman wrote:
> >
> > 3. Right click and add a "composite" widget to the workspace
> 
> I was wondering why the composite locus was needed, but then I realized that
> you were planning on executing the composite as a whole.
> 
> Of course, scripts/WFD's should be executable without first being composited.
> Is that what the 'execute script' option is for?
> 
> Scripts/WFD's should be compositable at any point: The first step need not be
> to make a composite.

Brad, I was wrong about this, and you were right.

Recall that command-line loci (executable name, flags, filenames, etc.) are
connected via 'string-adding' connectors.  Well, considering ordinary 'loci' by
definition can be anywhere on the Internet, it doesn't make sense to consider
these command-line loci ordinary.  The problem is, how would you do
'string-adding' across the Internet?  And does it even make sense to try it,
because these loci are soooo simple.

So, I propose that we define a special locus/widget that is like a composite
locus but contains only command-line loci.

Going back to our old example (where I was beginning to see the need to
separate these special loci) we have a 'command-line composite locus':

                           +----------+
                  ----->(1)|          |(3)<------
                 (2)<------| x-povray |(4)<------
                           |          |
+--------------------------+----------+----------------------------+
|    |   (2)                             |                  |      |
|    |   /|\                             |                  |      |
|   \|/   |                             \|/                \|/     |
|   (1)   |                             (3)                (4)     |
|+-----------+      +------+        +---------+        +---------+ |
|| processor | ---> | flag | -----> | infile  | -----> | infile  | |
|+-----------+      +------+        +---------+        +---------+ |
|| x-povray  |      |  -I  |                                       |
|+-----------+      +------+                                       |
+------------------------------------------------------------------+

  (1) & (2) are workflow I/O using command-line stdin/stdout.
  (3) & (4) provide the command line with the local (UNIX commands
            work with local files) location of the input files.

Cheers.
Jeff
-- 
                      +----------------------------------+
                      |           J.W. Bizzaro           |
                      |                                  |
                      | http://bioinformatics.org/~jeff/ |
                      |                                  |
                      |        BIOINFORMATICS.ORG        |
                      |           The Open Lab           |
                      |                                  |
                      |    http://bioinformatics.org/    |
                      +----------------------------------+