--- a/CADDSuite-1.6/galaxyconfigs/tools/upload.xml	Sat Dec 15 13:16:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<?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>