planemo questions

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planemo questions

Christian Brenninkmeijer
Hi All,

If there is a separate planemo mailing list please point me there.

I have been planing with planemo and find it a great tools.

This gives me two questions.

1. Why does planemo lint say:
"CHECK: Help contains valid reStructuredText."
But not throw an error when there is NO such information

2. Is there a way to do a test when there are multiple output files.
For example a tool ways writes to two different files.

Thanks in advance
Christian


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Re: planemo questions

Peter Cock
On Mon, Apr 27, 2015 at 5:23 PM, Christian Brenninkmeijer
<[hidden email]> wrote:
> Hi All,
>
> If there is a separate planemo mailing list please point me there.
>

Not that I am aware of, galaxy-dev seems fine.

> I have been planing with planemo and find it a great tools.
>
> This gives me two questions.
>
> 1. Why does planemo lint say:
> "CHECK: Help contains valid reStructuredText."
> But not throw an error when there is NO such information

By default planemo prints out when checks it does. You can
use the optional arguments to make it less talkative, e.g.

$ planemo lint --report_level warn my_tool_folder

I would expect planemo to warn/error if the tool has no help.

> 2. Is there a way to do a test when there are multiple output files.
> For example a tool ways writes to two different files.

(This isn't a planemo specific question)

Yes, just use multiple <output> tags within the <test>, e.g.

https://github.com/peterjc/pico_galaxy/blob/master/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml

Peter
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