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.


<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 != ""

<param name="dbkey" type="genomebuild" label="Genome" />
       <conditional name="files_metadata" title="Specify metadata"
value_ref="file_type" value_ref_in_group="False" />


        <data name="output" format="txt" />


I am not sure where I am making a mistake... Is the procedure to upload a
file for java different from python?

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