Re: [galaxy-dev] Intergrate custom script with multiple outputs

[Carlos Borroto]

On Wed, Oct 9, 2013 at 12:10 PM, UMD Bioinformatics
 wrote:
> Hi Carlos,
>
> I've done some more tinkering and it seems that you are correct about passing 
> the additional inputs. I can run the program with two inputs but if I use the 
> repeat element $inputs on my command it fails. Where do I need to implement 
> your suggestion? in the XML, or script, or both? Here is my updated XML file 
> that works with just two inputs.
>

In your xml, this should work:

  bkgd_sbtr_ian_properoutput.py $column $output1 $output1.id $input1 $input2
#for $i in $inputs
  ${i.input}
#end for


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Re: [galaxy-dev] Intergrate custom script with multiple outputs

[UMD Bioinformatics]

Hi Carlos,

I've done some more tinkering and it seems that you are correct about passing 
the additional inputs. I can run the program with two inputs but if I use the 
repeat element $inputs on my command it fails. Where do I need to implement 
your suggestion? in the XML, or script, or both? Here is my updated XML file 
that works with just two inputs.

Cheers
Ian



jose_bkgd.xml
Description: XML document



On Oct 9, 2013, at 10:11 AM, Carlos Borroto  wrote:

> Hi Ian,
> 
> As far as I can tell you problem could be the files not being written
> to the right place. From the link you posted:
> "To use this method at least one output dataset (output1 in our
> example) must be specified - this dataset will act as the reference
> for our additional datasets. The new additional datasets must be
> placed in the directory provided by $__new_file_path__ and named in
> the form:"
> 
> Although there is also this possibility:
> "Alternately, if your universe_wsgi.ini has collect_outputs_from =
> job_working_directory, moving the files into $__new_file_path__ is not
> needed and only the naming form above is required."
> 
> Please confirm you have the proper setting in universe_wsgi.ini or try
> telling your tool to write all outputs files to $__new_file_path__.
> 
> Also, I didn't know you could use $inputs(a repeat element definition
> in your xml) in that way. I thought you needed to do something like
> this:
> #for $i in $inputs
>  ${i.input}
> #end for
> 
> Hope it helps,
> Carlos
> 
> On Wed, Oct 9, 2013 at 8:48 AM, UMD Bioinformatics
>  wrote:
>> Hello,
>> 
>> I'm trying to incorporate a python tool that can accommodate multiple input
>> files and the number of output files cannot be determined prior to running
>> the tool. I've been though the help section at
>> http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
>> but I'm not getting any results. The tool isn't even running and creating
>> the proper output in the tool directory. I've felt with the naming
>> convention requited by Galaxy and the tool works from the command line. I
>> know that the issue isn't with my local Galaxy install because a generic
>> tool I've installed that produces multiple outputs works fine. I've attached
>> my code and the XML file. Any help would be appreciated.
>> 
>> 
>> 
>> 
>> Cheers
>> Ian
>> 
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Re: [galaxy-dev] Intergrate custom script with multiple outputs

[UMD Bioinformatics]

Hi Carlos,

Well first I fixed my typo but it still doesn't work. I do have my 
universe_wsgi.ini set to use the job_working_directory and I've test this with 
a functional script to make sure that was not the issue. I found the $inputs 
XML setup in another Galaxy script. It takes the additional files but maybe 
it's not passing them properly? 

This is the error I'm getting
/bin/sh: galaxy.tools.DatasetFilenameWrapper: No such file or directory

Ian
On Oct 9, 2013, at 10:11 AM, Carlos Borroto 
 wrote:

> Hi Ian,
> 
> As far as I can tell you problem could be the files not being written
> to the right place. From the link you posted:
> "To use this method at least one output dataset (output1 in our
> example) must be specified - this dataset will act as the reference
> for our additional datasets. The new additional datasets must be
> placed in the directory provided by $__new_file_path__ and named in
> the form:"
> 
> Although there is also this possibility:
> "Alternately, if your universe_wsgi.ini has collect_outputs_from =
> job_working_directory, moving the files into $__new_file_path__ is not
> needed and only the naming form above is required."
> 
> Please confirm you have the proper setting in universe_wsgi.ini or try
> telling your tool to write all outputs files to $__new_file_path__.
> 
> Also, I didn't know you could use $inputs(a repeat element definition
> in your xml) in that way. I thought you needed to do something like
> this:
> #for $i in $inputs
>  ${i.input}
> #end for
> 
> Hope it helps,
> Carlos
> 
> On Wed, Oct 9, 2013 at 8:48 AM, UMD Bioinformatics
>  wrote:
>> Hello,
>> 
>> I'm trying to incorporate a python tool that can accommodate multiple input
>> files and the number of output files cannot be determined prior to running
>> the tool. I've been though the help section at
>> http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
>> but I'm not getting any results. The tool isn't even running and creating
>> the proper output in the tool directory. I've felt with the naming
>> convention requited by Galaxy and the tool works from the command line. I
>> know that the issue isn't with my local Galaxy install because a generic
>> tool I've installed that produces multiple outputs works fine. I've attached
>> my code and the XML file. Any help would be appreciated.
>> 
>> 
>> 
>> 
>> Cheers
>> Ian
>> 
>> ___
>> 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/
>> 
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>>  http://galaxyproject.org/search/mailinglists/
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> 
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Re: [galaxy-dev] Intergrate custom script with multiple outputs

[Carlos Borroto]

Hi Ian,

As far as I can tell you problem could be the files not being written
to the right place. From the link you posted:
"To use this method at least one output dataset (output1 in our
example) must be specified - this dataset will act as the reference
for our additional datasets. The new additional datasets must be
placed in the directory provided by $__new_file_path__ and named in
the form:"

Although there is also this possibility:
"Alternately, if your universe_wsgi.ini has collect_outputs_from =
job_working_directory, moving the files into $__new_file_path__ is not
needed and only the naming form above is required."

Please confirm you have the proper setting in universe_wsgi.ini or try
telling your tool to write all outputs files to $__new_file_path__.

Also, I didn't know you could use $inputs(a repeat element definition
in your xml) in that way. I thought you needed to do something like
this:
#for $i in $inputs
  ${i.input}
#end for

Hope it helps,
Carlos

On Wed, Oct 9, 2013 at 8:48 AM, UMD Bioinformatics
 wrote:
> Hello,
>
> I'm trying to incorporate a python tool that can accommodate multiple input
> files and the number of output files cannot be determined prior to running
> the tool. I've been though the help section at
> http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
> but I'm not getting any results. The tool isn't even running and creating
> the proper output in the tool directory. I've felt with the naming
> convention requited by Galaxy and the tool works from the command line. I
> know that the issue isn't with my local Galaxy install because a generic
> tool I've installed that produces multiple outputs works fine. I've attached
> my code and the XML file. Any help would be appreciated.
>
>
>
>
> Cheers
> Ian
>
> ___
> 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/
>
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Re: [galaxy-dev] Intergrate custom script with multiple outputs

[Peter Briggs]

Hi Ian

Not sure if this is the cause of the problem but the interpreter 
specified in the  tag of your XML has a typo i.e. you have 
"pytyhon" rather than "python". I'm guessing this is why the tool 
doesn't run?


HTH, best wishes

Peter

On 09/10/13 13:48, UMD Bioinformatics wrote:

Hello,

I'm trying to incorporate a python tool that can accommodate multiple
input files and the number of output files cannot be determined prior to
running the tool. I've been though the help section at
http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
 but
I'm not getting any results. The tool isn't even running and creating
the proper output in the tool directory. I've felt with the naming
convention requited by Galaxy and the tool works from the command line.
I know that the issue isn't with my local Galaxy install because a
generic tool I've installed that produces multiple outputs works fine.
I've attached my code and the XML file. Any help would be appreciated.


Cheers
Ian


--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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