On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga <khm...@soe.ucsc.edu> wrote:

> Hi Greg,
>    Thanks for the feedback. I cannot seem to find information for
> hmmdb.loc.  When I look in the associated xml file it looks like it could
> be removed completely (does one need a precompiled HMM Database? I do not
> remember using anything like this when I run hmmer on the commandline).  I
> have less experience with changing wrappers, etc. Have you tried just
> commenting this part out?  And do I need to start the instance over to test
> it?
> Thanks in advance!
> - Karen
>     <conditional name="hmmdb">
>         <param name="select" type="select" label="HMM Db">
>           <option value="db" selected="True">Precompiled HMM
> Database</option>
>           <option value="user">HMM Database in your History</option>
>         </param>
>         <when value="db">
>             <param name="file" type="select" label="Precompiled HMM
> database">
>                 <options from_file="hmmdb.loc">
>                     <column name="name" index="1"/>
>                     <column name="value" index="2"/>
>                 </options>
>             </param>
>         </when>
>         <when value="user">
>             <param name="file" type="data" format="hmmer" label="HMM
> database" />
>         </when>
>     </conditional>

This lets the Galaxy HMMER wrapper either be used with system level
HMM databases (listed in hmmer.loc, e.g. PFAM) or with the user's own
HMM databases in their current history.

[This is very similar to how the BLAST+ wrappers work.]

If you don't have or need any standard HMM databases (e.g. PFAM)
then an empty hmmer.loc file should work fine. Try that first.

However, the tool author ought to provide an example named
hmmer.loc.sample which explains how to set this up - it looks
like two columns, description and filename.

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