How can I tell what programs are used by a tool?
Hi all -- I'd like to know what programs are used when I run a tool on my data. Ideally I'd also like to know what parameters are passed to command line tools. For example, I uploaded a sam file to the main galaxy server at PSU. I ran Filter Indels. I got output. What programs were used in this manipulation? samtools mpileup? GATK? FASTX toolkit? I hope I'm missing something extremely obvious. Thanks for your help. Holly
On Tue, Feb 7, 2012 at 9:52 PM, Beale, Holly (NIH/NHGRI) [F] <holly.beale@nih.gov> wrote:
Hi all --
I'd like to know what programs are used when I run a tool on my data. Ideally I'd also like to know what parameters are passed to command line tools.
The short answer is you can't, other than by reading the tool's documentation (ideally within Galaxy below the options), and/or reading the tool's source code (the XML file plus any scripts). Some Galaxy tools are simple wrappers for a single command line tool, in which case it is usually clear how the parameters offered to you in the Galaxy interface translate to matching command line arguments. Such Galaxy tools should make this clear in their documentation, along with giving you clear citation information for the underlying tools. Other Galaxy tools are complex scripts/tools that may call several other command line tools internally So it depends. Peter
Thank you Peter. That's great to know. On Feb 7, 2012, at 5:13 PM, Peter Cock wrote:
On Tue, Feb 7, 2012 at 9:52 PM, Beale, Holly (NIH/NHGRI) [F] <holly.beale@nih.gov> wrote:
Hi all --
I'd like to know what programs are used when I run a tool on my data. Ideally I'd also like to know what parameters are passed to command line tools.
The short answer is you can't, other than by reading the tool's documentation (ideally within Galaxy below the options), and/or reading the tool's source code (the XML file plus any scripts).
Some Galaxy tools are simple wrappers for a single command line tool, in which case it is usually clear how the parameters offered to you in the Galaxy interface translate to matching command line arguments. Such Galaxy tools should make this clear in their documentation, along with giving you clear citation information for the underlying tools.
Other Galaxy tools are complex scripts/tools that may call several other command line tools internally
So it depends.
Peter
participants (2)
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Beale, Holly (NIH/NHGRI) [F] -
Peter Cock