I added an attribute "format_source" (analogous to metadata_source) to the <data> tag to deal with that kind of issue: see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
<inputs> <param name="input" type="data" format="sff,fasta,fastq" label="454 reads" /> <param name="qual_file" type="data" format="qual" optional="true" label="Quality reads file (if input is a fasta)" /> </inputs>
<outputs> <data name="output" format_source="input" label="${tool.name} on ${on_string}: cleaned reads"/> <data name="out_qual" format_source="qual_file" label="${tool.name} on ${on_string}: cleaned reads"> <filter>qual_file != None</filter> </data> </outputs>
JJ
Hi everyone,
I'm facing a little problem ...
I have the following input :
<param name="input" type="data" format="sff,fasta,fastq" label="454 reads" /> <param name="qual_file" type="data" format="qual" optional="true" label="Quality reads file (if input is a fasta)" />
and the following output: <data name="output" format="input" label="${tool.name} on ${on_string}: cleaned reads"/> <data name="out_qual" format="qual" label="${tool.name} on ${on_string}: cleaned reads"> <filter>qual_file != None</filter>
</data>
If I provide the tool a sff file, the output is sff, if I only provide a fasta file and no qual file the output will be a fasta. However if I provide a fasta+qual the output will be considered as qual file even if it's a fasta file.
I don't get how it can mark my output file as a qual file knowing it's not a valid input file format.
Any ideas ? thx,
Jerome