comparison synapse_query.xml @ 2:a104cc98359c

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2:a104cc98359c

<tool id="synapse_query" name="Synapse Query" version="1.0">
	<description>Query Synapse</description>
	<command interpreter="python">$script_file
#if str( $user ) != '':
  -u "$user"
#end if    

#if str( $pass ) != '':
  -p "$pass"
#end if    
-o $outfile
	</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="txt" name="outfile" />
	</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"
));

query <- "${query}";
cat(query)
if ( !is.null(opt\$user) && !is.null(opt\$pass)) {
	synapseLogin(username=user, password=pass)
}

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

"""
import tempfile
import os
import sys
import subprocess

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

proc = subprocess.Popen( ["Rscript", path] + sys.argv[1:], 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>
</tool>