On Mon, Dec 13, 2010 at 5:18 PM, Peter <peter@maubp.freeserve.co.uk> wrote:
Hi all,
I'm trying to sort out some final details for my FASTQ filter by ID script before uploading it to the tool shed. This tool takes two input files, a FASTQ file (can be any type of FASTQ) and a tabular file (which has the IDs to filter on). The output file(s) are are also FASTQ (of the same variant as the input FASTQ file). I had simply used something like this when defining my outputs:
<data name="output_pos" format="fastq" label="With matched ID" /> <data name="output_neg" format="fastq" label="Without matched ID" />
However, this discards the fact that the input (and therefore my output) may have been fastqsanger or fastqillumina etc. According to the wiki http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax I can use format="input" in this setting... but here I have TWO input files (of different formats). Although this isn't giving an error, I find this results in my output being treated as tabular:
<data name="output_pos" format="input" label="With matched ID" /> <data name="output_neg" format="input" label="Without matched ID" />
I've also tried using the names of my input parameters, but that is just treated as a new file format (interestingly no error is raised):
<data name="output_pos" format="input_fastq" label="With matched ID" /> <data name="output_neg" format="input_fastq" label="Without matched ID" />
How is format="input" meant to work? Is it currently restricted to the special case of only one input file? Can you specify which input file somehow, e.g. via metadata_source?
I found that format="input" did work when I had one and only one input file format (see my "Divide FASTQ file into paired and unpaired reads" tool just uploaded to the 'Galaxy Tool Shed'). Is there some undocumented trick like format="input:paramname" where you can specify the input parameter name? Thanks, Peter