<commit_before>use strict;
use Data::Dumper;
use Carp;

=head1 NAME

    find_interactions_with_inferelator - Network Inference for cMonkey output

=head1 SYNOPSIS

    find_interactions_with_inferelator [--url=http://172.16.17.32:7079/ --ws=<workspace name for run result> --series=<expression data series reference> --cmonkey=<cmonkey run result reference> --tflist=<regulators list reference> --user=<username> --pw=<password>]

=head1 DESCRIPTION

    Inferelator discovers regulators for biclusters found by cMonkey in gene expression profiles.

=head2 Documentation for underlying call

    Returns Job object ID. This Job object will keep workspace reference to InferelatorRunResult when the run will be finished.

=head1 OPTIONS

=over 6

=item B<--url>=I<http://172.16.17.32:7079/>
    the service url 

=item B<-h> B<--help>
    print help information

=item B<--version>
    print version information

=item B<--ws>
    workspace name where run result will be stored

=item B<--series>
    Workspace reference to ExpressionSeries object

=item B<--cmonkey>
    Workspace reference to CmonkeyRunResult object

=item B<--tflist>
    Workspace reference to GeneList object with IDs of regulatory genes

=item B<--user>
    User name

=item B<--pw>
    Password

=back

=head1 EXAMPLE

    find_interactions_with_inferelator --url=http://172.16.17.32:7079/ --ws="AKtest" --series="AKtest/Halobacterium_sp_NRC1_series" --cmonkey="AKtest/kb|cmonkeyrunresult.132" --tflist="AKtest/kb|genelist.5" --user=<username> --pw=<password>
    find_interactions_with_inferelator --help
    find_interactions_with_inferelator --version

=head1 VERSION

    1.0

=cut

use Getopt::Long;
use Bio::KBase::cmonkey::Client;
use Bio::KBase::AuthToken;
use Bio::KBase::AuthUser;

my $usage = "Usage: find_interactions_with_inferelator [--url=http://172.16.17.32:7079/ --ws=<workspace name for run result> --series=<expression data series reference> --cmonkey=<cmonkey run result reference> --tflist=<regulators list reference> --user=<username> --pw=<password>]\n";

my $url        = "http://172.16.17.32:7079/";
my $ws         = "";
my $series     = "";
my $cmonkey    = "";
my $tflist     = "";
my $user       = "";
my $pw         = "";
my $help       = 0;
my $version    = 0;

GetOptions("help"       => \$help,
           "version"    => \$version,
           "ws=s"    => \$ws,
           "series=s"    => \$series,
           "cmonkey=s"    => \$cmonkey,
           "tflist=s"    => \$tflist,
           "user=s"    => \$user,
           "pw=s"    => \$pw,
           "url=s"     => \$url) <commit_msg>fixed bug in perl script<commit_after>use strict;
use Data::Dumper;
use Carp;

=head1 NAME

    find_interactions_with_inferelator - Network Inference for cMonkey output

=head1 SYNOPSIS

    find_interactions_with_inferelator [--url=http://172.16.17.32:7079/ --ws=<workspace name for run result> --series=<expression data series reference> --cmonkey=<cmonkey run result reference> --tflist=<regulators list reference> --user=<username> --pw=<password>]

=head1 DESCRIPTION

    Inferelator discovers regulators for biclusters found by cMonkey in gene expression profiles.

=head2 Documentation for underlying call

    Returns Job object ID. This Job object will keep workspace reference to InferelatorRunResult when the run will be finished.

=head1 OPTIONS

=over 6

=item B<--url>=I<http://172.16.17.32:7079/>
    the service url 

=item B<-h> B<--help>
    print help information

=item B<--version>
    print version information

=item B<--ws>
    workspace name where run result will be stored

=item B<--series>
    Workspace reference to ExpressionSeries object

=item B<--cmonkey>
    Workspace reference to CmonkeyRunResult object

=item B<--tflist>
    Workspace reference to GeneList object with IDs of regulatory genes

=item B<--user>
    User name

=item B<--pw>
    Password

=back

=head1 EXAMPLE

    find_interactions_with_inferelator --url=http://172.16.17.32:7079/ --ws="AKtest" --series="AKtest/Halobacterium_sp_NRC1_series" --cmonkey="AKtest/kb|cmonkeyrunresult.132" --tflist="AKtest/kb|genelist.5" --user=<username> --pw=<password>
    find_interactions_with_inferelator --help
    find_interactions_with_inferelator --version

=head1 VERSION

    1.0

=cut

use Getopt::Long;
use Bio::KBase::inferelator::Client;
use Bio::KBase::AuthToken;
use Bio::KBase::AuthUser;

my $usage = "Usage: find_interactions_with_inferelator [--url=http://172.16.17.32:7079/ --ws=<workspace name for run result> --series=<expression data series reference> --cmonkey=<cmonkey run result reference> --tflist=<regulators list reference> --user=<username> --pw=<password>]\n";

my $url        = "http://172.16.17.32:7079/";
my $ws         = "";
my $series     = "";
my $cmonkey    = "";
my $tflist     = "";
my $user       = "";
my $pw         = "";
my $help       = 0;
my $version    = 0;

GetOptions("help"       => \$help,
           "version"    => \$version,
           "ws=s"    => \$ws,
           "series=s"    => \$series,
           "cmonkey=s"    => \$cmonkey,
           "tflist=s"    => \$tflist,
           "user=s"    => \$user,
           "pw=s"    => \$pw,
           "url=s"     => \$url) 
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{'dir': 'git-commits-cleaned', 'id': '7240374', 'n_tokens_mistral': 1922, 'n_tokens_neox': 1779, 'n_words': 456}