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