I don't know anything about the tool or parameters in question , but it looks 
like the expected output filename is well formatted enough that you can derive 
it from the input filename and parameters.

You could write a small python wrapper to grant you full control over 
manipulating output files and finding/renaming them as you like, or, you could 
maybe try something like (and I have not tried this at all myself and have no 
idea what your parameters mean)  
from_work_dir="${input1}reads_l_${parameter1}_${parameter2}_CNTGS_DIST0_EM20.txt"

Good luck-

Dannon

On Dec 5, 2011, at 3:52 PM, Toqa Manasrah wrote:

> Thank you so much Dannon.
> I appreciate your help but I need some more clarification.
> 
> in the tool I am integrating (which is java classes) if the input parameters 
> are
> 
> ./main.bash  eps0.3_40reads.fa  population10_ref.fa 15 6 120
> 
> Then teh output is in eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt
> 
> As u notice the output file name is not specified in teh command line, and 
> actually I dont have the source files to go over this naming restriction.
> 
> how I can use from_work_dir attribute to tell galaxy this the file to display?
> 
> note: there are 11 output files and I am interested in this one only 
> ..._CNTGS_DIST0_EM20.txt
> 
> 
> any other method to overcome such problem  
> 
> I have presentation tomorrwo. hope things will work fine.
> 
> Thank you,
> ________________________________________
> From: Dannon Baker [dannonba...@me.com]
> Sent: Monday, December 05, 2011 2:41 PM
> To: Toqa Manasrah
> Subject: Re: [galaxy-dev]  Urgent help needed
> 
> Sure.  See the link in my previous email 
> (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) and look for 
> the <data> section for an explanation of the attributes available to you.  
> For an example of a tool that uses the from_work_dir element, see the 
> cufflinks, cuff compare, top hat, or trinity wrappers in your galaxy install.
> 
> -Dannon
> 
> 
> On Dec 5, 2011, at 2:25 PM, Toqa Manasrah wrote:
> 
>> Thank you Dannon,
>> I mean the first choice. no way to specify the output name in tool and it 
>> has many putputs but I am intereseted in one only.
>> 
>> Actually I dont know to use this attribute from_work_dir and I cant find 
>> help. can u help plz?
>> 
>> ________________________________________
>> From: Dannon Baker [dannonba...@me.com]
>> Sent: Monday, December 05, 2011 1:54 PM
>> To: Toqa Manasrah
>> Cc: galaxy-...@bx.psu.edu dev; Jennifer Jackson; galaxy-user
>> Subject: Re: [galaxy-dev]  Urgent help needed
>> 
>> Toqa,
>> 
>> Just to make sure I've understood your question: the problem is that a tool 
>> that you're trying to wrap doesn't provide a way to specify a particular 
>> output filename?  Take a look at the from_work_dir attribute of a <data> 
>> element.
>> 
>> Or are you asking how to define outputs in general?  For that, see the wiki 
>> at 
>> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set
>> 
>> Lastly, for new questions please start new email threads, instead of 
>> replying to old ones.  This makes it much easier for us to track our 
>> responses and make sure people get appropriate help.
>> 
>> -Dannon
>> 
>> 
>> On Dec 5, 2011, at 1:26 PM, Toqa Manasrah wrote:
>> 
>>> Hi Everybody,
>>> I am running a tool which is not defining the output file name as parameter.
>>> the tool is running and I can see the output file in the history directory 
>>> but not in the history frame.
>>> 
>>> how could I solve the problem? I should see and download the output file 
>>> from the history but I see an error message instead. the error message not 
>>> a real error but rather galaxy cannot figure out which file to display?
>>> 
>>> your help is appreciated,
>>> 
>>> 
>>> ________________________________________
>>> From: Jennifer Jackson [j...@bx.psu.edu]
>>> Sent: Tuesday, November 08, 2011 8:22 AM
>>> To: Toqa Manasrah
>>> Cc: Galaxy Dev
>>> Subject: Re: [galaxy-dev] Installing Galaxy on local server
>>> 
>>> Hello Tuqa,
>>> 
>>> Galaxy will not stop by itself. That said, you will want to monitor the
>>> instance and any associated cluster, just as you would any other
>>> important processes.
>>> 
>>> Please send all follow-up with a cc to the mailing list ("reply-all").
>>> The development community is a great resource for administrative advice
>>> and they may have more to add to this reply, i.e. how stable they have
>>> found Galaxy to be under various conditions.
>>> 
>>> Best,
>>> 
>>> Jen
>>> Galaxy team
>>> 
>>> On 11/8/11 4:01 AM, Toqa Manasrah wrote:
>>>> Thank you so much,
>>>> 
>>>> I did the installation and I ran it under my server.
>>>> I have one thing concerning about now. if u can help plz.
>>>> 
>>>> how to run Galaxy in such way that the html interface will continuously 
>>>> working and available for all users visiting the page?
>>>> 
>>>> i mean how to guarantee that the "sh run.sh" will keep running without any 
>>>> interrupt?
>>>> 
>>>> Thank you,
>>>> Tuqa
>>>> 
>>>> ________________________________________
>>>> From: Jennifer Jackson [j...@bx.psu.edu]
>>>> Sent: Thursday, November 03, 2011 6:47 PM
>>>> To: Toqa Manasrah
>>>> Cc: galaxy-...@bx.psu.edu
>>>> Subject: Re: [galaxy-dev] Installing Galaxy on local server
>>>> 
>>>> Hello Toqa,
>>>> 
>>>> From your description, this sounds like a local installation for the
>>>> Galaxy instance itself. Then you can add on a cluster (local or cloud)
>>>> as needed.
>>>> 
>>>> Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/
>>>> Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed
>>>> 
>>>> Hopefully the documentation is helpful,
>>>> 
>>>> Best,
>>>> 
>>>> Jen
>>>> Galaxy team
>>>> 
>>>> On 11/3/11 9:40 AM, Toqa Manasrah wrote:
>>>>> Hello,
>>>>> 
>>>>> I am a graduate student at GSU. I am looking for installing GALAXY on
>>>>> our local server http://alla.cs.gsu.edu/~software. as a result I like my
>>>>> server homepage start with the GALAXY interface, like this one:
>>>>> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some
>>>>> software tolls that we developed in ourdepartment. my primary question
>>>>> is which option Ihave to choose: Local or cloud?
>>>>> 
>>>>> looking forward for your help and directions.
>>>>> 
>>>>> Thank you.
>>>>> 
>>>>> Tuqa
>>>>> 
>>>>> 
>>>>> 
>>>>> ___________________________________________________________
>>>>> 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/
>>>> 
>>>> --
>>>> Jennifer Jackson
>>>> http://usegalaxy.org
>>>> http://galaxyproject.org/wiki/Support
>>>> 
>>> 
>>> --
>>> Jennifer Jackson
>>> http://usegalaxy.org
>>> http://galaxyproject.org/wiki/Support
>>> 
>>> ___________________________________________________________
>>> 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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