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1 <tool id="synapse_download" name="Synapse Download" version="1.0">
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2 <description>Download Synapse Entity</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 #if str( $pass ) != '':
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8 -p "$pass"
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9 #end if
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10 -s $synid
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11 $data_type
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12 -o $outfile
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13 </command>
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14 <inputs>
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15 <param name="user" type="text" size="90" label="Username"/>
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16 <param name="pass" type="text" size="90" label="Password"/>
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17 <param name="synid" type="text" label="Synapse ID"/>
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18 <param name="data_type" type="select" label="Data Type">
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19 <option value="-e">Affy Eset</option>
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20 <option value="-a">Attachment</option>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data format="txt" name="outfile" label="${synid}" />
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25 </outputs>
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26 <configfiles>
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27 <configfile name="script_file"><![CDATA[#!/usr/bin/env python
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28 rcode = """
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29 library('getopt');
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30 library(affy)
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31 require(synapseClient)
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32
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33 opt = getopt(c(
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34 'user', 'u', 2, "character",
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35 'pass', 'p', 2, "character",
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36 'outfile', 'o', 2, "character",
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37 'synid', 's', 2, "character",
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38 'eset', 'e', 0, "logical",
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39 'attach', 'a', 0, "logical"
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40 ));
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41
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42 if ( !is.null(opt\$user) && !is.null(opt\$pass)) {
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43 synapseLogin(username=user, password=pass)
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44 }
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45
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46 ent <- loadEntity(opt\$synid);
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47
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48 if (!is.null(opt\$eset)) {
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49 eset <- exprs(ent\$objects\$eset);
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50 write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file=opt\$outfile)
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51 write.table(eset, opt\$outfile, col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE);
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52 }
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53 if (!is.null(opt\$attach)) {
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54 fpath <- file.path(ent\$cacheDir, ent\$files[[1]]);
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55 file.copy(fpath, opt\$outfile, overwrite=T);
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56 }
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57
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58 """
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59
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60 import tempfile
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61 import os
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62 import sys
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63 import subprocess
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64
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65 h, path = tempfile.mkstemp()
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66 os.write(h,rcode)
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67 os.close(h)
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68
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69 print subprocess.check_output( ["Rscript", path] + sys.argv[1:], stderr=subprocess.STDOUT )
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70 os.unlink(path)
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71
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72 ]]></configfile>
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73 </configfiles>
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74 </tool>
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