[galaxy-dev] create multiple historie items

[Björn Grüning]

> 
> 	<outputs>
> 		<data name="output" format="interval"  />
> 	</outputs>
> 

Hi,

i think you simply need an extra output definition ala:

<data name="$output.id" format="interval"  />

Hope that helps.
Bjoern



> 
> 
> <help>
> **What it does**
> 
> # Parse igf formatted file and create wiggle tracks accordingly
> # Checks for existence of reserved filenames and check input formats
> 
> USAGE: ./GAPSS_igf2wig.v2.pl -i STRING -s BOOL -c INT
> 		
> 	Options:
> 	-i	REQ	IGF file 
> 	-s	OPT	Seperate strands [1=yes,0=no] DEFAULT=0
> 	-c	OPT	Cutoff for wig-file. Depths below this value are not printed.
> Zeros are never printed.	DEFAULT=1
> 
> 
> 
> 
> 
> This tool is based on `GAPSS` by Matt Hestand , Michiel van Galen and
> Michel Villerius.
> 
> http://www.lgtc.nl/GAPSS/    
> </help>
> </tool>
> ################END###############
> 
> #####cat galaxy-wrapper_GAPSS_igf2wig.v2.pl####
> #!/usr/bin/perl -w
> 
> my $galaxy_input             = $ARGV[0];
> my $SeperateStrands          = $ARGV[1];
> my $CutOff		     = $ARGV[2];
> my $galaxy_output            = $ARGV[3];
> my $galaxy_id		     = $ARGV[4];#not sure if whe need this var.
> 
> 
> system ("/usr/local/galaxy_dist/tools/NGS_tools_LUMC/GAPSS_igf2wig.v2.pl
> -i $galaxy_input -s $SeperateStrands -c $CutOff");
> 
> #when -s=0 only one file gets created and that end with _ALL.WIG.gz and
> this gets renamed to the galaxy_output var 
> #so far this works for one output file.
> system (" mv $galaxy_input\"_ALL.WIG.gz\" $galaxy_output ");
> 
> #when -s=1 two files get created  _FWD.WIG.gz and _REV.WIG.gz both these
> files needs to be imported as a history item
> #this part is what I don't get at the moment, I'm not sure if my .xml is
> giving all the right vars to do the job?
> #############END############
> 
> //Michel
> 
> On Wed, 2010-02-17 at 09:47 -0500, Anton Nekrutenko wrote:
> > Michel:
> > 
> > Can you just cut and paste GAPSS_igf2wig.v2.xml into e-mail directly.  
> > Thanks. a.
> > 
> > 
> > On Feb 17, 2010, at 9:49 AM, vill wrote:
> > 
> > > Thanks Anton,
> > >
> > > I really appreciate this. Attached is a gz file "gaps_igf2wig.tar.gz"
> > > with:
> > >
> > > *the perl script "GAPSS_igf2wig.v2.pl" that actually needs to be run
> > > *the perl wrapper script "galaxy-wrapper_GAPSS_igf2wig.v2.pl" that
> > > handles the .xml input and executes the perl script.
> > > *the .xml file "GAPSS_igf2wig.v2.xml"
> > > *a test input file "bowtie_format.igf"
> > >
> > > If you need anything else just let me know.
> > >
> > > //Michel
> > >
> > >
> > > On Wed, 2010-02-17 at 08:58 -0500, Anton Nekrutenko wrote:
> > >> Michel:
> > >>
> > >> Send us your wrapper and we'll take a look.
> > >>
> > >> Tx,
> > >>
> > >> anton
> > >> galaxy team
> > >>
> > >>
> > >> On Feb 17, 2010, at 8:56 AM, vill wrote:
> > >>
> > >>> I have a perl script that splits a text file with genomic  
> > >>> information
> > >>> (forward strand and reverse strand) in two separate files.
> > >>> One file for the forward strand and one file for the reverse strand.
> > >>>
> > >>> I have written a wrapper so that Galaxy can execute this script.
> > >>> When my script outputs one file this files is listed as a history
> > >>> item.
> > >>> When I let my script output the two files only one history item gets
> > >>> created.
> > >>>
> > >>> What I need to now is what extra variables do I need to output from
> > >>> the .xml file so that galaxy finds the two output files and puts  
> > >>> both
> > >>> files in as a history item
> > >>>
> > >>> I have been looking at the "interval2maf .py and .xml" I just can't
> > >>> figure out how this works, it seems that the history_id is important
> > >>> and
> > >>> the species is a list array and for every species a file gets
> > >>> created in
> > >>> the databas/tmp directory and when the file is created the tmp dir  
> > >>> is
> > >>> deleted.
> > >>> Adding and extra file from the .py into this tmp dir does not end up
> > >>> in
> > >>> the history items, renaming the files seems to end up with no  
> > >>> history
> > >>> items at all.
> > >>>
> > >>> Cheers,
> > >>>
> > >>> //Michel
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> galaxy-dev mailing list
> > >>> galaxy-dev at lists.bx.psu.edu
> > >>> http://lists.bx.psu.edu/listinfo/galaxy-dev
> > >>
> > >> Anton Nekrutenko
> > >> http://nekrut.bx.psu.edu
> > >> http://usegalaxy.org
> > >>
> > >>
> > >>
> > >
> > > <gaps_igf2wig.tar.gz>
> > 
> > Anton Nekrutenko
> > http://nekrut.bx.psu.edu
> > http://usegalaxy.org
> > 
> > 
> > 
> 
> 
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