Yes that's exactly what I ended up doing.
Please excuse any typos -- Sent from my iPhone
> On Apr 26, 2016, at 4:01 PM, Marius van den Beek <m.vandenb...@gmail.com>
> wrote:
>
> 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 <ngsbioinformat...@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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