<?xml version="1.0"?>

<tool name="Upload File" id="cadds_upload" version="1.1.2">
  <description>
    from your computer  
  </description>
  <action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
  <command interpreter="python">
      ../../../data_source/upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile
    #set $outnum = 0
    #while $varExists('output%i' % $outnum):
        #set $output = $getVar('output%i' % $outnum)
        #set $outnum += 1
        ${output.dataset.dataset.id}:${output.files_path}:${output}
    #end while
  </command>
  <inputs nginx_upload="true">
    <param name="file_type" type="select" label="File Format" help="Which format? See help below">
      <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ &quot;%s%s%s&quot; % ( line, self.separator, line ) for line in obj ]">
        <column name="value" index="1"/>
        <column name="name" index="0"/>
        <filter type="sort_by" column="0"/>
        <filter type="add_value" name="Auto-detect" value="auto" index="0"/>
      </options>
    </param>
    <param name="async_datasets" type="hidden" value="None"/>
    <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
      <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: For NGS and other large files (>~2GB), uploading via HTTP/FTP URL (below) is the most reliable method.">
        <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> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs -->
      </param>
      <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> 
      <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/>
      <!--
      <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."> 
        <option value="Yes">Yes</option>
      </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" />
    <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> -->
  </inputs>
  <help>

  </help>
</tool>