fix hisat2 extra outputs

[mblue9]

Sorry to be bringing hisat2 back again! but I just discovered that I accidentally left in a bracket that means that it's producing outputs that should be filtered out 😮 I left in the last bracket here:

<filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True) </filter>

I fixed it here. I also learnt that I can include to check that the correct number of outputs are produced so I've added that in.

(a slightly weird thing to me is that nothing complained about the stray bracket, not planemo lint, test or travis. I was wondering if something should or if I really do need to get myself some better 👀!)

[nsoranzo]

    <tests>
        <!-- Ensure bam output works -->

[nsoranzo]

I also learnt that I can include to check that the correct number of outputs are produced so I've added that in.

Good idea, thanks!

(a slightly weird thing to me is that nothing complained about the stray bracket, not planemo lint, test or travis. I was wondering if something should or if I really do need to get myself some better 👀!)

Unfortunately the behaviour of output filter is very weird: the expression is evaluated as Python code and if the result is True or an exception is raised, the filter is considered "passed" and the output dataset is added to the history.

[mblue9]

Thanks for the review and info @nsoranzo! I've fixed that comment position.

[nsoranzo]

Thanks @mblue9!