Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Ross
Hi, Jesse. >Yep, that's what I meant. Meaning that if I set that on my HTML file, >the extra_files would hopefully pick up the metadata from the >metadata_source. AFAIK, not possible. No metadata is stored anywhere in the Galaxy database tables for any of the files *inside* an html object files_

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Jesse Erdmann
On Tue, Nov 1, 2011 at 9:07 AM, Ross wrote: > On Tue, Nov 1, 2011 at 9:51 AM, Jesse Erdmann wrote: >> files visible in the first place and hide and link to the other items >> generated that aren't as likely to be reused is subsequent tasks.  The > > That sounds like a good way to use Html outputs

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Ross
On Tue, Nov 1, 2011 at 9:51 AM, Jesse Erdmann wrote: > files visible in the first place and hide and link to the other items > generated that aren't as likely to be reused is subsequent tasks.  The That sounds like a good way to use Html outputs - use the html history item to hide all the 'inform

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Jesse Erdmann
Sorry, I think I went a little too deep into the weeds and lost my way there last night. I think the answer is to just leave the BED/WIG files visible in the first place and hide and link to the other items generated that aren't as likely to be reused is subsequent tasks. The metadata, like which

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-10-31 Thread Jesse Erdmann
Thanks for the suggestions guys. I'm still struggling with a couple of things. How do I give the user a link to expose the file from extra_files_path as a history item and how would I set metadata like file format and db on the extra files? Things like PDF and text work fine, but I'd really like

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-10-31 Thread Ross
Hi, Jesse, IMHO, the Html datatype is perfect for this. By definition, the composite datatype can have any number of files (of any type!) in the files_path, but of course, your tool or wrapper will need to generate the legal html contents of that html page but that can be done when the files_path a

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-10-31 Thread Dannon Baker
Have you checked out the barcode splitter? The output is quite similar, an HTML report with links to the split files. -Dannon On Oct 31, 2011, at 2:50 PM, Jesse Erdmann wrote: > I have an in-house Perl tool that generates a double digit number of > outputs that we'd like the user to have acces

[galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-10-31 Thread Jesse Erdmann
I have an in-house Perl tool that generates a double digit number of outputs that we'd like the user to have access to, but don't necessarily need to be in the history. A complicating factor is that the exact number is determined at run time as user input can add any number of outputs that can't b