Hi Ryan,
I think you could create two regular outputs, and move the files to those outputs, i.e:
``` <command><![CDATA[ perl "$__tool_directory__"/doSomething.pl --sra "$sraid" && mv "${sraid}".data out.data && mv "${sraid}".txt out.txt ]]></command>
<inputs> <param name="sraid" ... /> </inputs>
<outputs> <data format="txt", name="out1" from_work_dir="out.data" /> <data format="txt", name="out2" from_work_dir="out.txt"/> </outputs> ```
I understand that you would also like to keep the $sraid id in the history, right? For that you should be able use `label="${sraid}.txt` on your outputs.
Cheers, Marius
On 26 April 2016 at 20:46, Ryan G ngsbioinformatics@gmail.com wrote:
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.
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