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
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-------------------------
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