<tool id="synapse_download" name="Synapse Download" version="1.0">
	<description>Download Synapse Entity</description>
	<command interpreter="python">$script_file
#if str( $user ) != '':
  -u "$user"
#end if
#if str( $pass ) != '':
  -p "$pass"
#end if    
-s $synid
$data_type
-o $outfile
	</command>
	<inputs>
		<param name="user" type="text" size="90" label="Username"/>
		<param name="pass" type="text" size="90" label="Password"/>
		<param name="synid" type="text" label="Synapse ID"/>
		<param name="data_type" type="select" label="Data Type">
			<option value="-e">Affy Eset</option>
			<option value="-a">Attachment</option>
		</param> 
	</inputs>
	<outputs>
		<data format="txt" name="outfile" label="${synid}" />
	</outputs>
	<configfiles>
        	<configfile name="script_file"><![CDATA[#!/usr/bin/env python
rcode = """
library('getopt');
library(affy)
require(synapseClient)

opt = getopt(c(
	'user', 'u', 2, "character",
	'pass', 'p', 2, "character",
	'outfile', 'o', 2, "character",
	'synid', 's', 2, "character",
	'eset', 'e', 0, "logical",
	'attach', 'a', 0, "logical"	
));

if ( !is.null(opt\$user) && !is.null(opt\$pass)) {
	synapseLogin(username=user, password=pass)
}

ent <- loadEntity(opt\$synid);

if (!is.null(opt\$eset)) {
	eset <- exprs(ent\$objects\$eset);
	write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file=opt\$outfile)
	write.table(eset, opt\$outfile, col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE);
}
if (!is.null(opt\$attach)) {
	fpath <- file.path(ent\$cacheDir, ent\$files[[1]]);
	file.copy(fpath, opt\$outfile, overwrite=T);
}

"""

import tempfile
import os
import sys
import subprocess

h, path = tempfile.mkstemp()
os.write(h,rcode)
os.close(h)

print subprocess.check_output( ["Rscript", path] + sys.argv[1:], stderr=subprocess.STDOUT )
os.unlink(path)

]]></configfile>
	</configfiles>
</tool>