The upload_dataset parameter type is very specific to the upload tool.
You may be able to make this work but it is not a supported feature
(meaning, we can't tell you how to do it). You probably want to use a
normal data input ("<input type='data' ..."). Users first upload
datasets to Galaxy using the upload tool, then run your tool on the
resulting dataset.

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Jun 18, 2013 at 11:48 AM, vijayalakshmi <v...@buffalo.edu> wrote:
> Hi all,
>
>    I have a tool written in java for which I want to upload a file as a
> parameter. I have trouble figuring out how to do it. I tried writing the xml
> file similar to 'tools/data-source/upload.xml' but it is not working.
>
> correlation.xml
>
> <tool id="correlation" name="Compute correlation" version="1.1.3">
>
>   <description> for the given BAM file </description>
>
>   <action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
>
>   <command>java -jar Correlation.jar $input_bam_file $output</command>
>
>   <inputs nginx_upload="true">
>
> <param name="async_datasets" type="hidden" value="None"/>
>
> <upload_dataset name="input" title="Specify Files for Dataset"
> file_type_name="file_type" metadata_ref="files_metadata">
> <param name="input_bam_file" type="file" size="30" label="File (Please avoid
> Windows format text file)" ajax-upload="true" help="TIP1: Due to browser
> limitations">
> <validator type="expression" message="You will need to reselect the file you
> specified (%s)." substitute_value_in_message="True">not ( ( isinstance(
> value, unicode ) or isinstance( value, str ) ) and value != "" )</validator>
> </param>
> </upload_dataset>
>
> <param name="dbkey" type="genomebuild" label="Genome" />
>        <conditional name="files_metadata" title="Specify metadata"
> value_from="self:app.datatypes_registry.get_upload_metadata_params"
> value_ref="file_type" value_ref_in_group="False" />
>
>   </inputs>
>
>   <outputs>
>         <data name="output" format="txt" />
>   </outputs>
>
> </tool>
>
>
> I am not sure where I am making a mistake... Is the procedure to upload a
> file for java different from python?
>
> Thanks,
> VJ.
>
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