Collection are one potential answer for how users can specify the set
of stuff that belongs in the directory. For explicitly dealing with
applications that consume directories - I think it is best to just
create the directory and link in files (if possible) before the tool
runs.
commandmkdir input_dir;
#for $i, $input_file in enumerate($input_files)# ln -s $input_file
input_dir/$i; #end for
my_application input_dir
/command
inputs
param name=input_files type=data format=bam multiple=true /
...
You can also do this sort of thing in a wrapper. If needed you can
build more interesting command-lines this way that add extensions, use
names, etc peptideshaker is an example of a fairly complex tool
that uses an idiom like this and doesn't resort to a helper wrapper
(https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=13a5bad5c984db6f#).
I am currently working on support for tools that actually produce
collections of files this way - I think I will probably land up adding
some high-level utilities for doing stuff like this for those
scenarios. But if you tool just produces a couple files and consume a
directory - no need to necessarily resort to collections (as the tool
author - your users will probably want to if they want to use these
tools in workflows).
-John
On Tue, Sep 2, 2014 at 9:51 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
You might be able to do this by accepting a collection of
SAM/BAM files as input instead. This is a quite new feature
in Galaxy, see:
https://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution
Peter
On Wed, Sep 3, 2014 at 10:00 AM, Philippe Moncuquet
philippe.m...@gmail.com wrote:
Hi,
I am trying to write a wrapper for a tool that take a directory containing
SAM/BAM files as an input. I am not sure how to do that, is there another
tool that implements this and that I can have a look at ? Any suggestions
would be greatly appreciated.
Regards,
Philip
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
