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Yabish - csplit optional positional argument #26

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
When trying to run csplit I get:

ccgmac005:trunk andrew$ yabish csplit -b "%02d.txt" -z -k -f aa -n 4 
yabi_tests/data/clustaltestseq.fa "/\\>/"
Staging in 1.3 KB in 0 directories and 1 files.
  Staging in file: clustaltestseq.fa (1.3 KB).
Staging in finished.
Running your job on the server.
An error occured: 
    Tool expects 3 positional arguments (repeat, PATTERN, inputFile) but 2 (scp://andrew@faramir.localdomain:22/export/home/tech/macgregor/stagein/d03113c7-22d7-11e0-b697-0017f2d30a14/clustaltestseq.fa, /\>/) were passed in.
ccgmac005:trunk andrew$ 

Does yabish allow for optional positionals?

Original issue reported on code.google.com by ahunter.ccg@gmail.com on 7 Jul 2011 at 7:18

GoogleCodeExporter commented 9 years ago 
A similar problem with genscan. This tool takes a positional argument outfile 
and then uses a redirect switch type to redirect the output into a file.

ccgmac005:trunk andrew$ yabish genscan /opt/genscan/1.0/lib/HumanIso.smat 
yabi_tests/data/genscan_files/genscan.fasta -v -cds -subopt 0.01 -ps genscan.ps 
2 genscan.txt
Staging in 227.8 KB in 0 directories and 1 files.
  Staging in file: genscan.fasta (227.8 KB).
Staging in finished.
Running your job on the server.
An error occured: 
    Tool expects 5 positional arguments (scale, psfname, cutoff, seqfname, parfname) but 6 (/opt/genscan/1.0/lib/HumanIso.smat, scp://andrew@faramir.localdomain:22/export/home/tech/macgregor/stagein/b00bea11-2464-11e0-bbe0-0017f2d30a14/genscan.fasta, 0.01, genscan.ps, 2, genscan.txt) were passed in.

Original comment by ahunter.ccg@gmail.com on 7 Jul 2011 at 7:18

GoogleCodeExporter commented 9 years ago

Original comment by aahun...@gmail.com on 7 Jul 2012 at 3:45