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1 <tool id="synapse_query" name="Synapse Query" version="1.0">
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2 <description>Query Synapse</description>
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3 <command interpreter="python">$script_file
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4 #if str( $user ) != '':
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5 -u "$user"
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6 #end if
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7
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8 #if str( $pass ) != '':
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9 -p "$pass"
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10 #end if
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11 -o $outfile
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12 </command>
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13 <inputs>
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14 <param name="user" type="text" size="90" label="Username"/>
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15 <param name="pass" type="text" size="90" label="Password"/>
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16 <param name="query" type="text" area="True" size="5x35" label="Query">
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17 <sanitizer>
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18 <valid initial="string.printable">
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19 <remove value="""/>
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20 </valid>
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21 <mapping initial="none">
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22 <add source=""" target="'"/>
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23 </mapping>
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24 </sanitizer>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data format="txt" name="outfile" />
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29 </outputs>
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30 <configfiles>
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31 <configfile name="script_file"><![CDATA[#!/usr/bin/env python
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32 rcode="""
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33 library('getopt');
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34 library(affy)
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35 require(synapseClient)
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36
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37 opt = getopt(c(
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38 'user', 'u', 2, "character",
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39 'pass', 'p', 2, "character",
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40 'outfile', 'o', 2, "character"
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41 ));
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42
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43 query <- "${query}";
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44 cat(query)
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45 if ( !is.null(opt\$user) && !is.null(opt\$pass)) {
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46 synapseLogin(username=user, password=pass)
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47 }
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48
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49 query.out <- synapseQuery(query);
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50 write.table(query.out, quote=F, file=opt\$outfile, row.name=F, sep="\\t")
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51
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52 """
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53 import tempfile
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54 import os
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55 import sys
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56 import subprocess
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57
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58 h, path = tempfile.mkstemp()
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59 os.write(h,rcode)
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60 os.close(h)
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61
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62 proc = subprocess.Popen( ["Rscript", path] + sys.argv[1:], stderr=subprocess.PIPE, stdout=subprocess.PIPE )
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63 (stdoutdata, stderrdata) = proc.communicate()
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64 if proc.returncode:
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65 sys.stderr.write(stderrdata)
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66 sys.stdout.write(stdoutdata)
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67 os.unlink(path)
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68
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69
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70 ]]></configfile>
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71 </configfiles>
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72 </tool>
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