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1 <tool id="synapse_download" name="Synapse Download" version="2.0.0">
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1
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2 <description>Download Synapse Entity</description>
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3
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3 <command interpreter="python">$script_file</command>
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1
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4 <inputs>
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5 <param name="user" type="text" size="90" label="Username"/>
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6 <param name="pass" type="text" size="90" label="Password"/>
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7 <param name="synid" type="text" label="Synapse ID"/>
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8 <param name="data_type" type="select" label="Data Type">
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9 <option value="e">Affy Eset</option>
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10 <option value="a">Attachment</option>
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="outfile" label="${synid}" />
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15 </outputs>
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16 <configfiles>
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17 <configfile name="script_file"><![CDATA[#!/usr/bin/env python
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18 rcode = """
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19 library(affy)
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20 require(synapseClient)
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21
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22 galaxyClean <- function(x) {
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23 y = gsub("__gt__", ">", x);
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24 y = gsub("__lt__", "<", y );
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25 y = gsub("__sq__", "'", y);
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26 y = gsub("__dq__", "\\"",y);
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27 y = gsub("__ob__", "[", y);
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28 y = gsub("__cb__", "]", y);
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29 y = gsub("__oc__", "{", y);
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30 y = gsub("__cc__", "}", y);
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31 y = gsub("__at__", "@", y);
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32 y = gsub("__cn__", "\\n", y);
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33 y = gsub("__cr__", "\\r", y);
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34 y = gsub("__tc__", "\\t", y);
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35 y = gsub("__pd__", "#", y);
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36 y = gsub("__at__", "@", y);
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37 return(y);
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1
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38 }
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39
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40 if (nchar("$user") && nchar("$pass")) {
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41 synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass"))
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42 }
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43
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1
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44
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45 cat("Loading...")
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46 ent <- loadEntity("$synid");
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47 cat("Done\n")
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48
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49 if ("e" == "$data_type") {
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50 eset <- exprs(ent\$objects\$eset);
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51 write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file="$outfile")
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52 write.table(eset, "$outfile", col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE);
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53 }
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54 if ("a" == "$data_type") {
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55 fpath <- file.path(ent\$cacheDir, ent\$files[[1]]);
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56 file.copy(fpath, "$outfile", overwrite=T);
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57 }
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58
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59 """
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60
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61 import tempfile
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62 import os
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63 import sys
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64 import subprocess
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65
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66 h, path = tempfile.mkstemp()
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67 os.write(h,rcode)
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68 os.close(h)
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69
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70 cmd_args = ["R", "CMD", "BATCH", path ]
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71 proc = subprocess.Popen(cmd_args, stderr=subprocess.PIPE)
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72 stdout, stderr = proc.communicate()
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73 if proc.poll() != 0:
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74 sys.stderr.write(stderr)
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1
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75 os.unlink(path)
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76 ]]></configfile>
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77 </configfiles>
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3
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78 <help>
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79
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80 This tool current supports two types of data from Synapse: Affy eset data and attachment files.
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81 For Affy eset data, it will attempt to turn the eset into a table and write a tab separated file. For attachment files, it will
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82 save the first attached file as the output.
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83
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84 Install R SynapseClient::
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85
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86 source('http://depot.sagebase.org/CRAN.R')
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87 pkgInstall("synapseClient")
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88
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89 `To setup auto login (so you don't have to type in your password) <https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login>`_
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90
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91 </help>
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92 </tool> |
