Hi Michel,
One thing there is a typo in the title, Multple -> should be Multiple.
Fixed, thanks :)
Last thing how do I find out which version nr. of Galaxy I'm Running on?
Assuming you are using mercurial, you can enter "hg head" at the command line when inside of your galaxy clone.
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:
The first thing to check here is that the fields are separated by tabs (not spaces -- some text editors make this less than apparent). Thanks, Dan On Feb 18, 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
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