On Thu, Oct 31, 2013 at 11:02 AM, Alexandre Loywick <a.loyw...@gmail.com> wrote:
> Thank you for your fast answer Peter,
>
> The thing is I have some constraints about this developpement and creating
> multiple tools for similar processes is a bit annoying so...
>
> I'm not really aware of macros in the xml, I'll go read the wiki again about
> that.
>
> bests,
> Alexandre

In addition to the wiki documentation, for a complex set of examples
Bjoern and John have used the macros to remove a LOT of duplication
in the BLAST+ XML files,
https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus

The repeated snippets are defined here:
https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml

Note there are two kinds, XML and tokens - the tokens are new and
not yet on the wiki. They can be used inside the Cheetah syntax for
the <command> tag and also the RST markup for the <help> tag.

In a simple case (and the older BLAST+ versions) we'd just reference
the macros file from the individual tools with:

    <macros>
        <import>ncbi_macros.xml</import>
    </macros>

You insert the XML macros with lines like this:

<expand macro="input_conditional_choose_db_type" />

This is fairly easy (although it can be harder to debug).

Peter
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