Thanks for the answer, so I tryed to write a wrapper, but the main script is not recognize. When I'm calling my wrapper in the xml file, I don't have to specify the full path but then from my wrapper if I want to call my main script I can't if this one is not on the PATH ? the wrapper current directory is the job_working_directory, there is anyway to access my main script just like it's done for the wrapper ? thanks for your answer, Jerome Peter Cock a écrit :
On Mon, Jun 6, 2011 at 2:45 PM, Mariette <jmariett@toulouse.inra.fr> wrote:
Hi everyone,
I'm new in galaxy and I want to create a component, so I have multiple questions. The component executes a script which takes different formats : fasta|fastq|sff. As output it takes a folder, to do so I used the extra_files_path attribute of an output data (--out='$output.extra_files_path'). The result file is stored in this folder with the log file and should be in the same format as the input one. I wrote the xml file and it works just fine, however as it's a folder there is no way to use the result file(s) for further analysis. How can I manage this ?
I use a wrapper script which moves the output file from the sub-directory to the location Galaxy requested.
Regarding the file format, if you only have one input file you can use format="input", otherwise use the change_format tag in the XML.
Also it can happen that there is more than 1 file outputted, how can I manage multiple outputs ?
An other question about the input format, I have an option to the script to specify the format. I saw there is auto-format detection routines in galaxy, there is a way so I can call them to automatically complete this option ?
Normally the wrapper specifies the output format explicitly.
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: