<tool id="synapse_query" name="Synapse Query" version="1.0">
	<description>Query Synapse</description>
	<command interpreter="python">$script_file</command>
	<inputs>
		<param name="user" type="text" size="90" label="Username"/>
		<param name="pass" type="text" size="90" label="Password"/>
		<param name="query" type="text" area="True" size="5x35" label="Query"/>
		
		<!--
			<sanitizer>
				<valid initial="string.printable">
					<remove value="&quot;"/>
				</valid>
				<mapping initial="none">
					<add source="&quot;" target="&apos;"/>
				</mapping>
			</sanitizer>
		</param>
		-->		
	</inputs>
	<outputs>
		<data format="tabular" name="outfile" />
	</outputs>
	<configfiles>
        	<configfile name="script_file"><![CDATA[#!/usr/bin/env python
rcode="""
library(affy)
require(synapseClient)

galaxyClean <- function(x) { 
y = gsub("__gt__", ">", x);
y = gsub("__lt__", "<", y );
y = gsub("__sq__", "'", y);
y = gsub("__dq__", "\\"",y);
y = gsub("__ob__", "[", y);
y = gsub("__cb__", "]", y);
y = gsub("__oc__", "{", y);
y = gsub("__cc__", "}", y);
y = gsub("__at__", "@", y);
y = gsub("__cn__", "\\n", y);
y = gsub("__cr__", "\\r", y);
y = gsub("__tc__", "\\t", y);
y = gsub("__pd__", "#", y);
y = gsub("__at__", "@", y);
return(y);
}

if (nchar("$user") && nchar("$pass")) {
	synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass"))
}



query <- galaxyClean("${query}");
cat(query)

query.out <- synapseQuery(query);
write.table(query.out, quote=F, file="$outfile", row.name=F, sep="\\t")

"""
import tempfile
import os
import sys
import subprocess

h, path = tempfile.mkstemp(dir="/tmp")
os.write(h,rcode)
os.close(h)

proc = subprocess.Popen( ["Rscript", path], stderr=subprocess.PIPE, stdout=subprocess.PIPE )
(stdoutdata, stderrdata) = proc.communicate()
if proc.returncode:
	sys.stderr.write(stderrdata)
sys.stdout.write(stdoutdata)
os.unlink(path)

]]></configfile>
	</configfiles>
		<help>

Install R SynapseClient::

    source('http://depot.sagebase.org/CRAN.R')
    pkgInstall("synapseClient")

`To setup auto login (so you don't have to type in your password) &lt;https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login&gt;`_ 

Example Query:

select * from entity where parentId=="syn300013"

	</help>

</tool>