| Previous changeset 1:7a60e992bfb0 (2012-07-24) Next changeset 3:93c4d2fad9af (2012-10-24) |
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added:
synapse_query.xml |
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| diff -r 7a60e992bfb0 -r a104cc98359c synapse_query.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/synapse_query.xml Tue Jul 24 17:34:37 2012 -0400 |
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| @@ -0,0 +1,72 @@ +<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 $outfile + </command> + <inputs> + <param name="user" type="text" size="90" label="Username"/> + <param name="pass" type="text" size="90" label="Password"/> + <param name="query" type="text" area="True" size="5x35" label="Query"> + <sanitizer> + <valid initial="string.printable"> + <remove value="""/> + </valid> + <mapping initial="none"> + <add source=""" target="'"/> + </mapping> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="txt" name="outfile" /> + </outputs> + <configfiles> + <configfile name="script_file"><![CDATA[#!/usr/bin/env python +rcode=""" +library('getopt'); +library(affy) +require(synapseClient) + +opt = getopt(c( + 'user', 'u', 2, "character", + 'pass', 'p', 2, "character", + 'outfile', 'o', 2, "character" +)); + +query <- "${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> |