Hi Shaun,

This should be possible.  It's been quite a long time since I worked on tools, 
so maybe others can provide better assistance if I am incorrect here.  You'll 
need to have a conditional something like the following ( not tested whatsoever 
):

      <conditional name="selected_file_select_list">
          <param name="selected_gtf_file" type="select" label="Gtf file by 
species">
              <options from_file="some_file">
                <column name="name" index="2"/>
                <column name="some_value" index="1"/>
              </options>
          </param>
          <when value="some_value">
              <param name="values_from_selected_gtf_file" type="select" 
label="Values from selected gtf file" />
                <options from_file="some_value">
                        <column name="name" index="2"/>
                        <column name="some_value" index="1"/>
                </options>
          </when>
      </conditional>


On Jul 13, 2011, at 9:45 AM, SHAUN WEBB wrote:

> 
> Hi Greg, I'm not sure if this answers my question. Using options_from_file is 
> fine if I want to refer to the same file each time.
> 
> In this case I want the first select to choose which gtf file to look at (by 
> species) and the second select to pull options (gtf annotation types) from 
> this file.
> 
> So I would somehow have to reference the file using the first parameter 
> rather than giving a hard-coded path.
> 
> Is that possible?
> 
> Shaun
> 
> 
> Quoting Greg Von Kuster <g...@bx.psu.edu> on Wed, 13 Jul 2011 09:23:19 -0400:
> 
>> Hello Shaun,
>> 
>> Use the 'from_file' option.  The referenced file should be in the 
>> ~/tool-data directory in the Galaxy root.  There are several example tools 
>> in the distribution that use this option.  Here is the example code from the 
>> annotation profiler tool:
>> 
>> <param name="table_names" type="drill_down" display="checkbox" 
>> hierarchy="recurse" multiple="true" label="Choose Tables to Use" 
>> help="Selecting no tables will result in using all tables." 
>> from_file="annotation_profiler_options.xml"/>
>> 
>> and here is an example from the microbial import tool:
>> 
>>      <param name="kingdom" type="select" label="Select the Desired Kingdom">
>>        <options from_file="microbial_data.loc" startswith="ORG">
>>          <column name="name" index="3"/>
>>          <column name="value" index="3"/>
>>          <filter type="unique_value" name="unique" column="3"/>
>>        </options>
>>      </param>
>> 
>> 
>> On Jul 13, 2011, at 6:17 AM, SHAUN WEBB wrote:
>> 
>>> 
>>> Hi,
>>> 
>>> I am trying to write a tool xml file and want to do the following:
>>> 
>>> 
>>> I have a number of GTF files stored locally and referenced in a data table. 
>>> I give the user a drop down list of those available using the following 
>>> code:
>>> 
>>> <param name="gtf" type="select"  label="GTF File">
>>>   <options from_data_table="gtf_files"/>
>>> </param>
>>> 
>>> 
>>> I then want them to choose an annotation type based on those present in the 
>>> selected gtf file above. It seems simple enough to do this if the gtf file 
>>> is in your history already:
>>> 
>>> <param name="feature" type="select" multiple="true" label="Extract 
>>> features">
>>> 
>>> <options from_dataset="gtf">
>>> 
>>>  <column name="name" index="2"/>
>>> 
>>>  <column name="value" index="2"/>
>>> 
>>>  <filter type="unique_value" name="unique" column="2"/>
>>> 
>>>  </options>
>>> 
>>> </param>
>>> 
>>> 
>>> But is there a way to query locally stored files via datatables/.loc files 
>>> to pull out options when the file is dynamically chosen by a different 
>>> parameter?
>>> 
>>> This code is also wrapped in a conditional, I'm not sure if that will 
>>> affect anything.
>>> 
>>> Thanks
>>> Shaun
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> --
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>> 
>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>> 
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>> 
>> 
>> 
>> 
> 
> 
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> ___________________________________________________________
> 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/

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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