From agatorano@gmail.com Mon Jul 23 18:25:15 2012
From: Andre Gatorano <agatorano@gmail.com>
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] .loc file for tophat
Date: Mon, 23 Jul 2012 15:25:05 -0700
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 <CAOjtKWV=06U6TK3hBPDDHfFiFE+f+m6SHPKDh_cG9uqi1+xd1w@mail.gmail.com>
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Which .loc file corresponds to tophat? I looked through the .xml file for
the wrapper and it made no reference to any .loc file.

-- 
Andre Gatorano
847-845-9284
University of California San Diego



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From jeremy.goecks@emory.edu Wed Jul 25 12:18:16 2012
From: Jeremy Goecks <jeremy.goecks@emory.edu>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] .loc file for tophat
Date: Wed, 25 Jul 2012 11:18:06 -0500
Message-ID: <AB8AAFEF-160E-47BB-9998-56141D82B188@emory.edu>
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 <CAOjtKWV=06U6TK3hBPDDHfFiFE+f+m6SHPKDh_cG9uqi1+xd1w@mail.gmail.com>
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The key lines in the wrapper are:

--
<options from_data_table=3D"tophat_indexes">
        <filter type=3D"sort_by" column=3D"2"/>
        <validator type=3D"no_options" message=3D"No indexes are available fo=
r the selected input dataset"/>
</options>
--

This code refers to the tool_data_table_conf.xml file, where tophat_indexes i=
s defined:

--
<!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
    <table name=3D"tophat_indexes" comment_char=3D"#">
        <columns>value, dbkey, name, path</columns>
        <file path=3D"tool-data/bowtie_indices.loc" />
    </table>
--

So you can see that Tophat uses the tool-data/bowtie_indices.loc file, which =
is reasonable because these tools share the same index format.

Best,
J.

On Jul 23, 2012, at 5:25 PM, Andre Gatorano wrote:

> Which .loc file corresponds to tophat? I looked through the .xml file for t=
he wrapper and it made no reference to any .loc file.=20
>=20
> --=20
> Andre Gatorano
> 847-845-9284
> University of California San Diego
>=20
> ___________________________________________________________
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