Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows

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Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows

ANGELICA GOMEZ ROIG
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__()


2014-04-04 6:05 GMT+02:00 Jennifer Jackson <[hidden email]>:

Reply posted:
http://dev.list.galaxyproject.org/known-name-outputs-shown-in-database-files-but-not-in-galaxy-windows-tt4664079.html

Angelica,
Next time it would be great to post to only a single list. The [hidden email] list is best for this type of question.
Take care,
Jen
Galaxy team


On 4/3/14 12:13 AM, ANGELICA GOMEZ ROIG wrote:
I have made a wrapper that has a tool that giving it an input file, gives you two output files with known extension: .gem and .log
I call the tool with a python file, and I pass it the input file and the two output file names for galaxy to show them, but when I look into de database/files/000/ i get four files:
 
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)
 
So,what I'm getting in the galaxy interface is  _54.dat and _55.dat, both empty, instead of _54.dat.gem and _54.dat.log that are the good ones.  How can I fix these?
Thanks


___________________________________________________________
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-- 
Jennifer Hillman-Jackson
http://galaxyproject.org



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Re: Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows

Peter Cock
On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
<[hidden email]> 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: Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows

John Chilton-4
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 <[hidden email]> wrote:

> On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
> <[hidden email]> 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
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Re: Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows

ANGELICA GOMEZ ROIG
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 <[hidden email]>:
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 <[hidden email]> wrote:
> On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
> <[hidden email]> 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/