Hi Olaf,

it seems that you know on forehand which files are going to be
generated, it might be wise that when this script is run under galaxy
that you are able to set the filenames for each file using additional
comandline arguments.

If this is not the case, then you should follow the naming convention
for each additional file as mentioned here:
__new_file_path__/"%s_%s_%s_%s_%s" % ( 'primary', output1.id, name,
'visible', file_type )

This would mean in your xml:
<command>
PedCount.pl $input -post -count -write $PC1_Counts -prefix
"${__new_file_path__}/primary_${PC1_Counts.id}_"
</command>
...
<outputs>
     <data format="txt" name="PC1_Counts" />
</output>

In your script you can then do:
getoptions(
...,
prefix => \$prefix,
write => \$basefile,
);
open(my $F, ">",$basefile);
print $F "Writing to primary file;"
for $i (0..$#loop){
     open (my $A, ">",$prefix.'_'.$i);
     print $A "Writing to additional file";
     close $A;
}

This will put all your additional files in the galaxy history.

Maybe there is a better way, but this is how I use it to split certain
files in multiple files.

Cheers,
Jelle

On Tue, Mar 9, 2010 at 8:27 PM, Stein, Olaf
<Olaf.Stein@nationwidechildrens.org> wrote:
> Sorry, but I am still having issues:
>
> Here is my history:
>  empty, format: txt,  database: ?
> <http://10.70.250.254:8080/root/edit?id=41>
>
> Info: $Id: PedCount.pl 2408 2009-11-13 17:29:39Z whv001 $
> -post flag seen
> -count flag seen
> -write seen, using
> "/export/home/galaxy/galaxy-dist/database/files/000/dataset_41.dat" prefix
> Marker set 1
> Bucketizing reduces evaluation count from 1140 to 470, or by 58
>
>
> And my config file:
> <tool id="PedCount" name="PedCount Step" force_history_refresh="True">
>   <description>Combines structurally identical pedigrees into counted bins
> to simplify analysis.</description>
>   <command interpreter="perl">PedCount.pl $input -post -count -write
> $PC1_Counts $PC1_Pedigrees</command>
>   <inputs>
>     <param format="txt" name="input" type="data" label="Post MAKEPED file"/>
>   </inputs>
>   <outputs>
>     <data format="txt" name="PC1_Counts" />
>     <data format="txt" name="PC1_Pedigrees" />
>   </outputs>
>
>   <help>
>     Combines structurally identical pedigrees into counted bins to simplify
> analysis.
>   </help>
> </tool>
>
>
> And the data on disk, it is where the history says it is, I just don’t know
> how to get to it through galaxy:
> -rw-rw-r-- 1 galaxy galaxy   668 Mar  9 14:32 dataset_41.dat1_Config.Dat
> -rw-rw-r-- 1 galaxy galaxy  2595 Mar  9 14:32 dataset_41.dat1_Counts.Dat
> -rw-rw-r-- 1 galaxy galaxy   160 Mar  9 14:32 dataset_41.dat1_Data.Dat
> -rw-rw-r-- 1 galaxy galaxy   263 Mar  9 14:32 dataset_41.dat1_Map.Dat
> -rw-rw-r-- 1 galaxy galaxy   662 Mar  9 14:32 dataset_41.dat1_Markers.Dat
> -rw-rw-r-- 1 galaxy galaxy 13464 Mar  9 14:32 dataset_41.dat1_Pedigrees.Dat
>
> I am sure this is something trivial, like naming or so
>
> Olaf
>
>
>
> On 3/9/10 1:59 PM, "Daniel Blankenberg" <dan@bx.psu.edu> wrote:
>
> Hi Olaf,
>
> This link may be helpful:
> http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
>
> Let us know if you need more assistance,
>
> Dan
>
> On Mar 9, 2010, at 1:49 PM, Stein, Olaf wrote:
>
> I will try and be a little more specific.
> I have a tool, it runs and produces the output files it would produce on the
> shell.
>
> Here is the history:
> -------------------------------------------------------
> Info: $Id: PedCount.pl <http://PedCount.pl>  2408 2009-11-13 17:29:39Z
> whv001 $
> -post flag seen
> -count flag seen
> -write seen, using
> "/export/home/galaxy/galaxy-dist/database/files/000/dataset_25.dat" prefix
> Marker set 1
> Bucketizing reduces evaluation count from 1140 to 470, or by 58
> ------------------------------------------------------
>
> I can see the files on disk in :
> /export/home/galaxy/galaxy-dist/database/files/000/
>
>
> How can I view them from within galaxy, and download them
>
> Thanks
> Olaf
> -------------------------
> Olaf Stein
> DBA
> Battelle Center for Mathematical Medicine
> Nationwide Children's Hospital, The Research Institute
> 700 Children's Drive
> 43205 Columbus, OH
> phone: 1-614-355-5685
> cell: 1-614-843-0432
> email: olaf.stein@nationwidechildrens.org
> <x-msg://846/olaf.stein@nationwidechildrens.org>
>
>
> “I consider that the golden rule requires that if I like a program I must
> share it with other people who like it.”
> Richard M. Stallman
>
> ------ Forwarded Message
> From: Olaf Stein <olaf.stein@nationwidechildrens.org
> <x-msg://846/olaf.stein@nationwidechildrens.org> >
> Date: Tue, 09 Mar 2010 11:59:33 -0500
> To: "galaxy-user@lists.bx.psu.edu <x-msg://846/galaxy-user@lists.bx.psu.edu>
> " <galaxy-user@lists.bx.psu.edu <x-msg://846/galaxy-user@lists.bx.psu.edu> >
> Conversation: Output files
> Subject: Output files
>
> Hi all,
>
> I have a tool setup (a small perl script) and it runs fine, I get the output
> I would usually see in shell in the history.
> The script also generates some output files (at least in a normal run in the
> shell), where within galaxy can I see those?
>
> Thanks
> Olaf
>
>
>
>
> -------------------------
> Olaf Stein
> DBA
> Battelle Center for Mathematical Medicine
> Nationwide Children's Hospital, The Research Institute
> 700 Children's Drive
> 43205 Columbus, OH
> phone: 1-614-355-5685
> cell: 1-614-843-0432
> email: olaf.stein@nationwidechildrens.org
> <x-msg://846/olaf.stein@nationwidechildrens.org>
>
>
> “I consider that the golden rule requires that if I like a program I must
> share it with other people who like it.”
> Richard M. Stallman
>
> ------ End of Forwarded Message
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user
>
>
>
>
>
>
>
> -------------------------
> Olaf Stein
> DBA
> Battelle Center for Mathematical Medicine
> Nationwide Children's Hospital, The Research Institute
> 700 Children's Drive
> 43205 Columbus, OH
> phone: 1-614-355-5685
> cell: 1-614-843-0432
> email: olaf.stein@nationwidechildrens.org
>
>
> “I consider that the golden rule requires that if I like a program I must
> share it with other people who like it.”
> Richard M. Stallman
>
> _______________________________________________
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> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user
>
>