I'm playing around with creating a Galaxy wrapper for custom tool I've created. My tool takes a single parameter, and SRA ID. In command block, I have something like this:
<command>
${GALAXY_ROOT_DIR}/tools/mycustomtools/doSomething.pl --sra $sraid
</command>
<inputs>
<param name="sraid" ... />
</inputs>
<outputs>
<data format="txt", name="out1", from_work_dir="${sraid}.data" />
<data format="txt", name="out2", from_work_dir="${sraid}.txt" />
</outputs>
Galaxy doesn't like thr $sraid in the output. I see from the docs I need to use discover_datasets. It would be nice to use a parameter such as what I have to name output file as my script names output files use an input parameter as the base.