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
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
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
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
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
Have you tried adding another output definition? Two changes below, first another output element, second changing output.id to output_id ('.' has special meaning). On Feb 17, 2010, at 9:56 AM, vill wrote:
<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" /> <data name="output_id" format="txt" />
</outputs>
Actually yes, Once my per script gets executed with the wrapper script my two output files get created in the files/000/ as dataset_424.dat_FWD.WIG.gz and dataset_424.dat_REV.WIG.gz but I can't get these files into separate uniquely ID'd history items from which I can send the files off to the UCSC browser. code : <command interpreter="perl">galaxy-wrapper_GAPSS_igf2wig.v2.pl $input $SeperateStrands $CutOff $output $output_id1 $output_id2 </command> <data name="output_id1" format="interval"> <data name="output_id2" format="interval"> I must be doing something wrong within the xml file but I don't know what? //Michel On Wed, 2010-02-17 at 09:57 -0500, James Taylor wrote:
Have you tried adding another output definition?
Two changes below, first another output element, second changing output.id to output_id ('.' has special meaning).
On Feb 17, 2010, at 9:56 AM, vill wrote:
<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 $output_id</command> <inputs> <param name="input" type="data" label="IGF File input" /> <param name="SeperateStrands" type="select" help="on seperate strands" label="0 or 1"> <option value="0">0</option> <option value="1">1</option> </param> <param name="CutOff" type="select" help="Select Cutoff" label="Cutoff size" > <option value="1">1</option> <option value="0">0</option> </param>
</inputs>
<outputs> <data name="output" format="interval" /> <data name="output_id" format="txt" />
</outputs>
<outputs> <data name="output" format="interval" /> </outputs>
Hi, i think you simply need an extra output definition ala: <data name="$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
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
Thanks Dan for the link, Been looking for this information and could not find it, bookmarked ;) I'm going to read this and then enjoy galaxy even more. //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
Related to the thread below, is there a way to view some listing or map of the wiki? The "ToolsMultipleOutput" page -- and other wiki pages linked to from this forum -- would have come in handy awhile ago but I couldn't find them by clicking from the wiki home. Thanks, Josh -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of vill Sent: Wednesday, February 17, 2010 10:23 AM To: Daniel Blankenberg Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] create multiple historie items Thanks Dan for the link, Been looking for this information and could not find it, bookmarked ;) I'm going to read this and then enjoy galaxy even more. //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
Josh, The wiki provided on bitbucket has no searching capability, and we have not yet created our own site map. We know it's a problem and have figured out what to do about it. We'll get to it as soon as we can. Kelly On Wed 17 Feb 2010, at 11:55 AM, Lee, Joshua wrote:
Related to the thread below, is there a way to view some listing or map of the wiki? The "ToolsMultipleOutput" page -- and other wiki pages linked to from this forum -- would have come in handy awhile ago but I couldn't find them by clicking from the wiki home.
Thanks, Josh
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of vill Sent: Wednesday, February 17, 2010 10:23 AM To: Daniel Blankenberg Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] create multiple historie items
Thanks Dan for the link,
Been looking for this information and could not find it, bookmarked ;) I'm going to read this and then enjoy galaxy even more.
//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
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
however filter doesn't seem to work with conditionals' params (i.e. conditional_name.some_param; e.g. do_full_assembly.create_ace_file) :(
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
Hello, Does e.g. do_full_assembly['create_ace_file'] work? Dan On Feb 19, 2010, at 12:40 AM, Edward Kirton wrote:
however filter doesn't seem to work with conditionals' params (i.e. conditional_name.some_param; e.g. do_full_assembly.create_ace_file) :(
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
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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
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
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
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Daniel, I had spaces, changed this to a tab and now it works. Thanks to all for the help. //Michel On Thu, 2010-02-18 at 09:47 -0500, Daniel Blankenberg wrote:
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
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hello galaxy team, I tried the procedure described on the wiki page about multiple output for tools:
You may also find this link useful: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
The variables between the filter-tags seem to be only evaluated when they are not enclosed by a conditional in the inputs-section. Is this a known issue or am I just doing something wrong? Evaluation of a variable not enclosed by a conditional works fine. Thanks for any help, André Kahles
André, You can see an example of how to do this in the tool next_gen_conversion/solid2fastq.xml. Basically, you need to refer to the variable as follows: condition_name['variable_name']. This isn't obvious, so I'll be adding it to the wiki. Let us know if you need anything else. Regards, Kelly On Fri 26 Feb 2010, at 7:15 PM, Andre Kahles wrote:
Hello galaxy team,
I tried the procedure described on the wiki page about multiple output for tools:
You may also find this link useful: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
The variables between the filter-tags seem to be only evaluated when they are not enclosed by a conditional in the inputs-section. Is this a known issue or am I just doing something wrong? Evaluation of a variable not enclosed by a conditional works fine.
Thanks for any help,
André Kahles _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Thanks for all replies. Works like a charm. Best regards André On Feb 27, 2010, at 4:05 AM, Kelly Vincent wrote:
André,
You can see an example of how to do this in the tool next_gen_conversion/solid2fastq.xml. Basically, you need to refer to the variable as follows: condition_name['variable_name']. This isn't obvious, so I'll be adding it to the wiki.
Let us know if you need anything else.
Regards, Kelly
On Fri 26 Feb 2010, at 7:15 PM, Andre Kahles wrote:
Hello galaxy team,
I tried the procedure described on the wiki page about multiple output for tools:
You may also find this link useful: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
The variables between the filter-tags seem to be only evaluated when they are not enclosed by a conditional in the inputs-section. Is this a known issue or am I just doing something wrong? Evaluation of a variable not enclosed by a conditional works fine.
Thanks for any help,
André Kahles _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hello, Thanks for your help. While I have conditionals and filters working now, I've noticed the filter doesn't seem to work with the Boolean type. The workaround is simply changing the offending field to a Select type. test tool config: <tool id='output_filter_test' name='output filter test'> <description>test</description> <command interpreter='perl'>test.pl $two_outfiles $outfile1 $outfile2</command> <inputs> <param name='two_outfiles' type='boolean' truevalue='1' falsevalue='0' checked='true' label='Want second file'/> </inputs> <outputs> <data name='outfile1' format='txt'/> <data name='outfile2' format='txt'> <filter>two_outfiles == '1'</filter> </data> </outputs> <help> Test script. </help> </tool> it refers to this simple perl script: #!/jgi/tools/bin/perl die("Expected 3 args") unless @ARGV == 3; my ($two_files, $outfile1, $outfile2) = @ARGV; open(OUT, ">$outfile1") or die($!); print OUT "this is outfile 1\n"; close OUT; if ($two_files) { open(OUT, ">$outfile2") or die($!); print OUT "this is outfile 2\n"; close OUT; } exit 0;
I have some code that needs to dynamically retrieve files via the Galaxy web server. When I try an html "get" using "some.file" I receive the following error: "Could not find 'some.file' on the extra files path." When I specify "/some.file" I receive the following error: "This link may not be followed from within Galaxy." [returned by root.py] * What/where is this "extra files path"? * How can I retrieve files via the Galaxy server relative to its root? [baseurl does not seem to work for me.] Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 cell:717 668-3048 office:410-550-4629 www.cidr.jhmi.edu
Hello Ed, instead of:
<data name='outfile2' format='txt'> <filter>two_outfiles == '1'</filter> </data>
try: <data name='outfile2' format='txt'> <filter>two_outfiles == True</filter> </data> Let us know if this doesn't work for you or if you have further questions. Thanks, Dan On Mar 9, 2010, at 1:08 AM, Edward Kirton wrote:
Hello, Thanks for your help. While I have conditionals and filters working now, I've noticed the filter doesn't seem to work with the Boolean type. The workaround is simply changing the offending field to a Select type.
test tool config:
<tool id='output_filter_test' name='output filter test'> <description>test</description> <command interpreter='perl'>test.pl $two_outfiles $outfile1 $outfile2</command> <inputs> <param name='two_outfiles' type='boolean' truevalue='1' falsevalue='0' checked='true' label='Want second file'/> </inputs> <outputs> <data name='outfile1' format='txt'/> <data name='outfile2' format='txt'> <filter>two_outfiles == '1'</filter> </data> </outputs> <help> Test script. </help> </tool>
it refers to this simple perl script:
#!/jgi/tools/bin/perl
die("Expected 3 args") unless @ARGV == 3; my ($two_files, $outfile1, $outfile2) = @ARGV; open(OUT, ">$outfile1") or die($!); print OUT "this is outfile 1\n"; close OUT; if ($two_files) { open(OUT, ">$outfile2") or die($!); print OUT "this is outfile 2\n"; close OUT; } exit 0;
participants (11)
-
Andre Kahles -
Anton Nekrutenko -
Björn Grüning -
Daniel Blankenberg -
Dean Snyder -
Edward Kirton -
Edward Kirton -
James Taylor -
Kelly Vincent -
Lee, Joshua -
vill