<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@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
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev