===> Please use "Reply All" when responding to this email! <===

Dear Yan-Hui Li,

you have to make sure the output files (and location) are named by
Galaxy. It isn't enough to just have the output files in the right
output directory. Looking at the documentation of phyml it seems you
can't set your own output file names. This means you will have to
write a wrapper that renames the files after the tool has run - or
contact the author to include options to specify output file names.

A wrapper can be as simple as a bashscript that executes the tool and
after a succesful finish renames the output files to the output file
names Galaxy provides (as described in the tool configuration xml -
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set)

Cheers,
Jelle


2011/8/26 liyanhui607 <liyanhui...@163.com>:
>  ===> Please use "Reply All" when responding to this email! <===
>
>
> Hi All,
>
>
>
> We want to add a program “PhyML 3.0” to galaxy system. This software was for 
> phylogenetic developed by http://www.atgc-montpellier.fr/phyml/binaries.php. 
> It can run normally in Linux environment with a file for example named 
> “sample” as input and two files automatically named 
> “sample.phy_phyml_stats.txt” and “sample.phy_phyml_tree.txt” as outputs.
>
>
>
> However, after added it to galaxy system, we found that it can produce the 
> right result files in directory "/var/we/galaxy-dist/database/files/000”, but 
> they did not return to the web page where they are empty. So who can tell me 
> what is wrong?
>
>
>
> Another question, is java applet supported by galaxy system?
>
>
>
> Thank you very much!
>
>
>
> Best Wishes!
>
>
>
> Yan-Hui Li
>
>
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___________________________________________________________
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