Output Files

8.7 years ago by

Stein, Olaf • 100 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 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 "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 Date: Tue, 09 Mar 2010 11:59:33 -0500 To: "galaxy-user@lists.bx.psu.edu" <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 "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

ADD COMMENT • link written 8.7 years ago by Stein, Olaf • 100

Hi Olaf, This link may be helpful: http://bitbucket.org/galaxy/galaxy- central/wiki/ToolsMultipleOutput Let us know if you need more assistance, Dan

ADD REPLY • link written 8.7 years ago by Daniel Blankenberg ♦♦ 1.7k

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> PedCount.pl $input -post -count -write $PC1_Counts $PC1_Pedigrees <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 Hi Olaf, This link may be helpful: http://bitbucket.org/galaxy/galaxy- central/wiki/ToolsMultipleOutput Let us know if you need more assistance, Dan 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 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 _______________________________________________ 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

ADD REPLY • link written 8.7 years ago by Stein, Olaf • 100

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

ADD REPLY • link written 8.7 years ago by Jelle Scholtalbers • 360

And this would allow me to view the files within galaxy and download them as well? Or would it just show me the path to the file on disk? Olaf 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 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

ADD REPLY • link written 8.7 years ago by Stein, Olaf • 100

This will show your files in galaxy and you can indeed download/save them as well. btw this part in my example: open (my $A, ">",$prefix.'_'.$i); should be: open (my $A, ">",$prefix.'_'.$i.'_visible_yourFileType'); Jelle On Wed, Mar 10, 2010 at 2:33 PM, Stein, Olaf

ADD REPLY • link written 8.7 years ago by Jelle Scholtalbers • 360

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