The key lines in the wrapper are:
--
<options from_data_table="tophat_indexes">
<filter type="sort_by" column="2"/>
<validator type="no_options" message="No indexes are available for the
selected input dataset"/>
</options>
--
This code refers to the tool_data_table_conf.xml file, where tophat_indexes is
defined:
--
<!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
<table name="tophat_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="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 the
> wrapper and it made no reference to any .loc file.
>
> --
> Andre Gatorano
> 847-845-9284
> University of California San Diego
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
