From j.scholtalbers@gmail.com Mon Oct  4 03:30:33 2010
From: Jelle Scholtalbers <j.scholtalbers@gmail.com>
To: galaxy-dev@lists.galaxyproject.org
Subject:
 Re: [galaxy-dev] [galaxy-user] Undocumented tags for tool	configuration
Date: Mon, 04 Oct 2010 09:30:20 +0200
Message-ID: <AANLkTikt164z66hsGhuC_9FeDOhvnp4t45gpTkFdEYrA@mail.gmail.com>
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Hi Kelly,

thank you. I added this info also to the wiki for further reference.

Cheers,
Jelle


On Fri, Oct 1, 2010 at 6:07 PM, Kelly Vincent <kpvincent(a)bx.psu.edu> wrote:
> Jelle,
>
> (I've copied this to galaxy-dev since it's more appropriate to that one)
>
> The data table approach is fairly new, so there aren't too many examples
> yet, although more tools are being converted and will be available soon in
> the distribution. Basically, there are 3 steps to using it:
> 1. Modify tool_data_table_conf.xml to specify:
>        - the bowtie data table
>        - the column types in the loc file
>        - It should look something like this:
>            <table name="bowtie_indexes">
>                <columns>name, value</columns>
>                <file path="tool-data/bowtie_indices.loc" />
>            </table>
> 2. Create/modify the loc file to correspond with the column types specified
> in tool_data_table_conf.xml (in this example, the loc file doesn't have to
> be changed), though we are going to be changing the specification to
> <columns>value, dbkey, name, path</columns>
> 3. Modify the Bowtie wrapper to use the data table instead of the loc file
> directly, replacing this:
>                  <options from_file="bowtie_indices.loc">
>                    <column name="value" index="1" />
>                    <column name="name" index="0" />
>                  </options>
>        - with this:
>                  <options from_data_table="bowtie_indexes"/>
>
> The <actions> in the Bowtie wrapper is used in lieu of the deprecated <code>
> tag to set the dbkey of the output dataset. In bowtie_wrapper.xml, according
> to the first action block, if the refGenomeSource.genomeSource is "indexed"
> (not "history"), then it will assign the dbkey of the output file to be the
> same as that of the reference file. It does this by looking at through the
> loc file and finding the line that has the value that's been selected in the
> index dropdown box as column 1 of the loc file entry and using the dbkey, in
> column 0 (ignoring comment lines (starting with #) along the way).
>
> If refGenomeSource.genomeSource is "history", it resorts to default behavior
> for Galaxy, which is that the output is assigned the same value as the first
> input that has a dbkey specified.
>
> The second block would not be needed for most cases--it is required here to
> handle the specific case of a small reference file we use for functional
> testing. It says that if the dbkey has been set to "equCab2chrM" (that's
> what the <filter type="metadata_value"... column="1" /> tag) does then it
> should be changed to "equCab2" (the <option type="from_param" ... column="0"
> ...> tag does).
>
> If you need more information than this, let us know.
>
> Regards,
> Kelly
>
>
>
> On Oct 1, 2010, at 4:22 AM, Jelle Scholtalbers wrote:
>
>> Hey,
>>
>> I was looking through the bowtie_wrapper.xml to get some information about
>> how to use the tool_data_table_conf.xml. There I also noticed in the output
>> section the tag <actions>.
>> Is there any information on this tag as is does seem to be used a lot?
>>
>> Cheers,
>> Jelle
>> _______________________________________________
>> galaxy-user mailing list
>> galaxy-user(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-user
>
>


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