Re: [Soaplab-users] Output files based on input argument

[Martin S. <mar...@gm...>]

I am sorry for a BIG delay in my reply. Somehow I forgot about this email...
In case you still do not have an answer...

I try to define output section for one of my tool but I cannot find the
>
right way:
>
> The tool takes a mandatory argument and returns three different files
> with names starting by the mandatory argument.
> e.g.:    input          ./tool --pdb=2SRC
>         outputs        2SRC.out, 2SRC.gff, 2SRC.bed
>
>
> How to properly code this in ACD format ?
>

Soaplab does not allow users to specify names of the output files (the
reasons are mostly because of the distributed character of web services
where the concept of "files" is blurred; but also some legacy reasons).
Therefore, if an application has to have a fixed names (either hard-coded
names or names based on other parameters, as it is in your example) one must
wrap the application into a wrapper script. The acd file specifies this
wrapper as an executable. The wrapper maps the fixed names into the names
generated by Soaplab. The wrapper knows what names were generated by Soaplab
because it gets the full command line created by Soaplab.

Here is an example - for the "cap3" program (
http://pbil.univ-lyon1.fr/cap3.php). The "cap3" program uses the name of its
input file as a prefix for several output file names. [In your example, the
prefix would be taken from the parameter "-pdb" and not from the input file
name.] The wrapper for cap3 program could use this command-line:

cap3_wrapper
     -I seq
     -q seq.qual
     -C seq.con

     -A seq.cap.ace
     -G seq.cap.contigs
     -Q seq.cap.contigs.qual
     -L seq.cap.contigs.links
     -F seq.cap.info
     -S seq.cap.singlets
     -R seq.con.cap.results

Where "-I" indicates the input file, and -A, -G, -Q, -L, -F, -S, and -R are
all possible output files. The ACD file will reflect this command-line. For
example, the first two outputs will be specified as:

...
outfile: ace [
  additional: "Y"
  qualifier: "A"
]

outfile: contigs [
  additional: "Y"
  qualifier: "G"
]
...

The wrapper itself (a Perl script) is attached (and included also below).

Cheers,
Martin

#!/usr/bin/perl -w
#
# Martin Senger <mar...@gm...>
# ---------------------------------------

use strict;
use Getopt::Std;
use vars qw/ $opt_H $opt_I $opt_q $opt_C $opt_A $opt_G $opt_Q $opt_L $opt_F
$opt_S $opt_R /;

$Getopt::Std::STANDARD_HELP_VERSION = 'true';
getopts ('HI:q:C:A:G:Q:L:F:S:R:');

sub HELP_MESSAGE() {
    print STDOUT <<'END_OF_USAGE';
cap3 seq [cap3-options]
     other (optional) inputs:
seq.qual
seq.con
     outputs:
standard output
seq.cap.ace
seq.cap.contigs
seq.cap.contigs.qual
seq.cap.contigs.links
seq.cap.info
seq.cap.singlets
seq.con.cap.results

cap3_wrapper
     -I seq
     -q seq.qual
     -C seq.con

     -A seq.cap.ace
     -G seq.cap.contigs
     -Q seq.cap.contigs.qual
     -L seq.cap.contigs.links
     -F seq.cap.info
     -S seq.cap.singlets
     -R seq.con.cap.results

Other:
-H ... help
END_OF_USAGE
    exit (0);
}

HELP_MESSAGE() if $opt_H;

# -----------------------------------------------------------

# -- change the input arguments
die "Required input file (option -I) is missing\n" unless defined $opt_I;
#my @cmdline = ('/home/senger/Software/CAP3/cap3', $opt_I);
my @cmdline = ('cap3', $opt_I);
push (@cmdline, @ARGV);

my $inp_qual = $opt_I . '.qual';
`cp $opt_q $inp_qual` if defined $opt_q && -e $opt_q;
my $inp_con = $opt_I . '.con';
`cp $opt_C $inp_con` if defined $opt_C && -e $opt_C;

# -- call the real cap3
system (@cmdline) == 0
    or die "Calling cap3 with the command line [" . join (" ", @cmdline) .
"] failed: $?\n";

# -- rename cap3's outputs
my $out_ace = $opt_I . '.cap.ace';
`mv $out_ace $opt_A` if -e $out_ace && defined $opt_A;
my $out_contigs = $opt_I . '.cap.contigs';
`mv $out_contigs $opt_G` if -e $out_contigs && defined $opt_G;
my $out_qual = $opt_I . '.cap.contigs.qual';
`mv $out_qual $opt_Q` if -e $out_qual && defined $opt_Q;
my $out_links = $opt_I . '.cap.contigs.links';
`mv $out_links $opt_L` if -e $out_links && defined $opt_L;
my $out_info = $opt_I . '.cap.info';
`mv $out_info $opt_F` if -e $out_info && defined $opt_F;
my $out_singlets = $opt_I . '.cap.singlets';
`mv $out_singlets $opt_S` if -e $out_singlets && defined $opt_S;
my $out_results = $opt_I . '.con.cap.results';
`mv $out_results $opt_R` if -e $out_results && defined $opt_R;


-- 
Martin Senger
email: mar...@gm...,mar...@ka...
skype: martinsenger