I added an example taken from trim.seqs.xml in the Mothur metagenomics tool_suite to: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax The following will create datasets in the history panel, setting the output data type to be the same as that of an input dataset named by the "format_source" attribute. Note that a conditional name is not included, so 2 separate conditional blocks should not contain parameters with the same name. <inputs> <!-- fasta may be an aligned fasta that subclasses Fasta --> <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/> <conditional name="qual"> <param name="add" type="select" label="Trim based on a quality file?" help=""> <option value="no">no</option> <option value="yes">yes</option> </param> <when value="no"/> <when value="yes"> <!-- qual454, qualsolid, qualillumina --> <param name="qfile" type="data" format="qual" label="qfile - a quality file"/> </when> </conditional> </inputs> <outputs> <data format_source="fasta" name="trim_fasta" label="${tool.name} on ${on_string}: trim.fasta"/> <data format_source="qfile" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual"> <filter>(qual['add'] == 'yes')</filter> </data> </outputs> On 6/9/11 2:39 AM, Peter Cock wrote:
On Wed, Jun 8, 2011 at 9:59 PM, Jim Johnson<johns198@umn.edu> wrote:
It went into galaxy-central:
$ hg log -pr 5082 changeset: 5082:a86e1fa82a89 user: Kanwei Li<kanwei@gmail.com> date: Thu Feb 17 15:35:07 2011 -0500 summary: Add a "format_source" attribute to the ToolConfig output data element [JJ Johnson]. Closes #470
...
And I should have put an example in: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Oh right - better late than never ;)
On the bright side because this commit was a while ago, it has already been included in the stable Galaxy releases.
Thanks for this, I can think of several of my own tools where this will work much more cleanly than the current solution using <change_format> and<when>.
Regards,
Peter