Re: [galaxy-dev] Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows
Thanks. Finally it worked!! I pass the solution:
My python file:
import sys,os
def __main__():
# Command to run GEM tool. Here the Gem indexer is getting invoked along
with arguments to be passed.
cmd=gem-indexer -i +sys.argv[1]+ -o +sys.argv[2]
os.system(cmd)
name_gem=sys.argv[2]+.gem
os.rename(name_gem,sys.argv[2])
if __name__ == __main__ : __main__()
Take care
2014-04-07 15:51 GMT+02:00 John Chilton jmchil...@gmail.com:
Just to add to what Peter said - you definitely don't want to use
from_work_dir and reference the outputs ($output1) in the same
command. If you know where the file is going to be relative to your
working directory there should be no reason to pass it to your script.
Also I think you want format instead of format_source as the attribute
on output.
On Mon, Apr 7, 2014 at 8:49 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
nirvanargr2...@gmail.com wrote:
Hi Jen,
I tried what you explain, but still doens't work.
I did create a new datatype, gem. And I modified my code as you
suggested.
The tool i'm using always generates by default two archives . gem and
.log.
Those are the ones that I can't show in the galaxy interface, the
output I
get is empty, the dataset_54.dat and the dataset_55.dat. I can't
handle to
show me the .dat.gem and .dat.log ones.
dataset_54.dat (my first declared output that it's empty)
dataset_54.dat.gem (the output that throws the tool)
dataset_54.dat.log (the other output file that throws the tool)
dataset_55.dat (my second declared output that it's empty)
Here it is the gem_indexer.xml
tool id=GEM Index name=create GEM Indexer
command interpreter=python gem_indexer.py $input $output1
$output2/command
inputs
param name=input type=data format=fasta label=Fichero de
entrada(formato .fas) /
/inputs
stdio
exit_code range=1: level=fatal description=Bad input
dataset
/
/stdio
outputs
data format_source=gem name=output1 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.gem /
data format_source=tab name=output2 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.log /
/outputs
/tool
And the gem_indexer.py
import sys,os
def __main__():
# Command to run GEM tool. Here the Gem indexer is getting invoked along
with arguments to be passed.
cmd=gem-indexer -i +sys.argv[1]+ -o salida
os.system(cmd)
if __name__ == __main__ : __main__()
Since you are using a wrapper script already, I would add
lines to rename the generated files (based on sys.argv[1]
plus the extensions) to the filename Galaxy is providing
(here sys.argv[2] and sys.argv[3]).
Peter
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Re: [galaxy-dev] Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows
On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
nirvanargr2...@gmail.com wrote:
Hi Jen,
I tried what you explain, but still doens't work.
I did create a new datatype, gem. And I modified my code as you suggested.
The tool i'm using always generates by default two archives . gem and .log.
Those are the ones that I can't show in the galaxy interface, the output I
get is empty, the dataset_54.dat and the dataset_55.dat. I can't handle to
show me the .dat.gem and .dat.log ones.
dataset_54.dat (my first declared output that it's empty)
dataset_54.dat.gem (the output that throws the tool)
dataset_54.dat.log (the other output file that throws the tool)
dataset_55.dat (my second declared output that it's empty)
Here it is the gem_indexer.xml
tool id=GEM Index name=create GEM Indexer
command interpreter=python gem_indexer.py $input $output1
$output2/command
inputs
param name=input type=data format=fasta label=Fichero de
entrada(formato .fas) /
/inputs
stdio
exit_code range=1: level=fatal description=Bad input dataset
/
/stdio
outputs
data format_source=gem name=output1 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.gem /
data format_source=tab name=output2 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.log /
/outputs
/tool
And the gem_indexer.py
import sys,os
def __main__():
# Command to run GEM tool. Here the Gem indexer is getting invoked along
with arguments to be passed.
cmd=gem-indexer -i +sys.argv[1]+ -o salida
os.system(cmd)
if __name__ == __main__ : __main__()
Since you are using a wrapper script already, I would add
lines to rename the generated files (based on sys.argv[1]
plus the extensions) to the filename Galaxy is providing
(here sys.argv[2] and sys.argv[3]).
Peter
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows
Just to add to what Peter said - you definitely don't want to use
from_work_dir and reference the outputs ($output1) in the same
command. If you know where the file is going to be relative to your
working directory there should be no reason to pass it to your script.
Also I think you want format instead of format_source as the attribute
on output.
On Mon, Apr 7, 2014 at 8:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
nirvanargr2...@gmail.com wrote:
Hi Jen,
I tried what you explain, but still doens't work.
I did create a new datatype, gem. And I modified my code as you suggested.
The tool i'm using always generates by default two archives . gem and .log.
Those are the ones that I can't show in the galaxy interface, the output I
get is empty, the dataset_54.dat and the dataset_55.dat. I can't handle to
show me the .dat.gem and .dat.log ones.
dataset_54.dat (my first declared output that it's empty)
dataset_54.dat.gem (the output that throws the tool)
dataset_54.dat.log (the other output file that throws the tool)
dataset_55.dat (my second declared output that it's empty)
Here it is the gem_indexer.xml
tool id=GEM Index name=create GEM Indexer
command interpreter=python gem_indexer.py $input $output1
$output2/command
inputs
param name=input type=data format=fasta label=Fichero de
entrada(formato .fas) /
/inputs
stdio
exit_code range=1: level=fatal description=Bad input dataset
/
/stdio
outputs
data format_source=gem name=output1 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.gem /
data format_source=tab name=output2 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.log /
/outputs
/tool
And the gem_indexer.py
import sys,os
def __main__():
# Command to run GEM tool. Here the Gem indexer is getting invoked along
with arguments to be passed.
cmd=gem-indexer -i +sys.argv[1]+ -o salida
os.system(cmd)
if __name__ == __main__ : __main__()
Since you are using a wrapper script already, I would add
lines to rename the generated files (based on sys.argv[1]
plus the extensions) to the filename Galaxy is providing
(here sys.argv[2] and sys.argv[3]).
Peter
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
