Michel, Your Bowtie loc file also needs to include the prefix of the index files themselves. So if you have the following files in the /data/ bowtie-genome-indexes/ directory: Human_UCSC_hg18.1.ebwt Human_UCSC_hg18.2.ebwt Human_UCSC_hg18.3.ebwt Human_UCSC_hg18.4.ebwt Human_UCSC_hg18.rev.1.ebwt Human_UCSC_hg18.rev.2.ebwt then your loc file entry should be: Human_UCSC_hg18 /data/bowtie-genome-indexes/Human_UCSC_hg18 Galaxy does not have version numbers as we don't do official releases. Instead we rely on the repo revision number, which you can get with the command hg heads in the repo dorectory. Regards, Kelly On Thu 18 Feb 2010, at 4:03 AM, vill wrote:
Thanks Daniel,
I got everything now working with the multiple output files (doing a victory dance ). One thing there is a typo in the title, Multple -> should be Multiple.
Next, I need Bowtie to run, we have our own index files, I edited the tool-data/bowtie-indices.loc file to point to my index files, only Galaxy does not see my index species? my bowtie-indices.loc file: ########## #Your bowtie_indices.loc file should include an entry per line for #each index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # #hg18 /depot/data2/galaxy/bowtie/hg18/hg18 #hg19 /depot/data2/galaxy/bowtie/hg19/hg19 Human_UCSC_hg18 /data/bowtie-genome-indexes/ Human_UCSC_hg19 /data/bowtie-genome-indexes/ Human_custom37 /data/bowtie-genome-indexes/ galGal3 /data/bowtie-genome-indexes/ e_coli /data/bowtie-genome-indexes/ ###########
Last thing how do I find out which version nr. of Galaxy I'm Running on?
//Michel
On Wed, 2010-02-17 at 10:08 -0500, Daniel Blankenberg wrote:
Hi Michel,
You may also find this link useful: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
Thanks,
Dan
On Feb 17, 2010, at 9:56 AM, vill wrote:
Sure,
Here is the .xml and the wrapper.
#######cat GAPSS_igf2wig.v2.xml########## <tool id="GAPSS_igf_2_WIG" name="GAPSS - IGF to WIG"> <description></description> <command interpreter="perl">galaxy-wrapper_GAPSS_igf2wig.v2.pl $input $SeperateStrands $CutOff $output $output.id</command> <inputs> <param name="input" type="data" label="IGF File input" /> <param name="SeperateStrands" type="select" help="on seperate strands" label="0 or 1"> <option value="0">0</option> <option value="1">1</option> </param> <param name="CutOff" type="select" help="Select Cutoff" label="Cutoff size" > <option value="1">1</option> <option value="0">0</option> </param>
</inputs>
<outputs> <data name="output" format="interval" /> </outputs>
<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
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev