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?
Thank you,
Peter