<?xml version="1.0"?>

<tool name="Upload expression array raw files" id="uploadAffy" >
  <description>
     Affymetrix .CEL or NimbleGen .XYS files in Zip file from your computer  
  </description>
  <action module="com.lilly.cistrome.upload" class="CistromeUploadToolAction"/>
  <command interpreter="python">
    upload.py $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>
    <param name="async_datasets" type="hidden" value="None"/>
    <param name="file_type" type="hidden" value="auto"/>
    <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: (Please read the instruction to prepare your Zip file)" ajax-upload="true"/> 
      <param name="url_paste" type="hidden" value=""/> 
      <param name="ftp_files" type="hidden" value="" label="Files uploaded via ASPERA"/>
      <param name="space_to_tab" type="hidden" value="Yes"/>
    </upload_dataset>
    <param name="dbkey" type="hidden" value="?"/>
    <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>
  <help>
  
**Syntax**

- **File** is a .zip archive containing .CEL or .XYS files, plus a .TXT pheno file.

-----

This tool allows you to upload sets of  Affymetrix .CEL or NimbleGen .XYS  files,   The file you upload must be a ZIP archive with a .zip extension containing  at least two .cel or .xys files (not both) and   there must be exactly one .txt (Tab delimited) phenotype file. The phenotype files should describe the data set and must contain a .Group. column with values 0 and 1 used to describe the members of sample and control groups.

Example of phenotype file::

    Sample            Key              Group
    1478-1-U133A-CEL  Down Syndrome    0
    748-1-U133A.CEL   Down Syndrome    0
    1218-1-U133A.CEL  Down Syndrome    0
    1389-1-U133A.CEL  Down Syndrome    0
    1479-1-U133A.CEL  Normal           1
    1521-1-U133A.CEL  Normal           1
    1390-1-U133A.CEL  Normal           1
    1411-1-U133A.CEL  Normal           1

The .zip archive will be shown in your Galaxy history after it is loaded. It can be used as input to the Gene Expression Index tool.

  </help>
</tool>