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 <vs49@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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