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3
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1 <tool id="synapse_create" name="Synapse Create" version="2.0.0">
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0
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2 <description>Create Synapse</description>
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3 <command interpreter="python">$script_file</command>
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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="name" type="text" size="90" label="Name"/>
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8 <param name="attachment" type="data" optional="true" label="Attachment"/>
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9 <param name="attachment_name" type="text" size="90" optional="true" label="Attachment Name"/>
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10 <param name="etype" type="select" label="Entity Type">
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11 <option value="Project">Project</option>
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12 <option value="Study">Study</option>
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13 <option value="Data">Data</option>
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14 </param>
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15 <repeat name="properties" title="Properties">
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16 <param name="name" type="select" size="90" label="Name">
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17 <option value="name">Name</option>
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18 <option value="parentId">ParentID</option>
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19 <option value="description">Description</option>
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20 <option value="species">Species</option>
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21 <option value="numSamples">Number of Samples</option>
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22 <option value="disease">Disease</option>
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23 <option value="tissueType">Tissue Type</option>
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24 </param>
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25 <param name="value" type="text" size="90" label="Value">
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26 <sanitizer>
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27 <valid initial="string.printable">
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28 <remove value="""/>
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29 </valid>
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30 <mapping initial="none">
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31 <add source=""" target="\""/>
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32 </mapping>
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33 </sanitizer>
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34 </param>
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35 </repeat>
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36
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37 <repeat name="annotations" title="Annotations">
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38 <param name="name" type="text" size="90" label="Name"/>
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39 <param name="value" type="text" size="90" label="Value">
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 <remove value="""/>
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43 </valid>
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44 <mapping initial="none">
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45 <add source=""" target="\""/>
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46 </mapping>
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47 </sanitizer>
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48 </param>
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49 </repeat>
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50
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51 </inputs>
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52 <outputs>
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53 <data format="txt" name="outfile" />
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54 </outputs>
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55 <configfiles>
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56 <configfile name="script_file"><![CDATA[#!/usr/bin/env python
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57 rcode="""
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58 require(synapseClient)
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59
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3
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60 galaxyClean <- function(x) {
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61 y = gsub("__gt__", ">", x);
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62 y = gsub("__lt__", "<", y );
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63 y = gsub("__sq__", "'", y);
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64 y = gsub("__dq__", "\\"",y);
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65 y = gsub("__ob__", "[", y);
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66 y = gsub("__cb__", "]", y);
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67 y = gsub("__oc__", "{", y);
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68 y = gsub("__cc__", "}", y);
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69 y = gsub("__at__", "@", y);
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70 y = gsub("__cn__", "\\n", y);
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71 y = gsub("__cr__", "\\r", y);
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72 y = gsub("__tc__", "\\t", y);
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73 y = gsub("__pd__", "#", y);
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74 y = gsub("__at__", "@", y);
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75 return(y);
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76 }
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77
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3
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78 if (nchar("$user") && nchar("$pass")) {
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79 synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass"))
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80 }
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81
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82
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83 ent <- ${etype}( list(name=galaxyClean("${name}")) )
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84
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85 #for $a in $annotations:
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86 annotValue(ent, galaxyClean("${a.name}")) <- galaxyClean("${a.value}")
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0
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87 #end for
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88
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89 #for a in $properties:
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90 propertyValue(ent, galaxyClean("${a.name}")) <- galaxyClean("${a.value}")
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91 #end for
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92
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93 ent <- createEntity(ent)
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94
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95 #if $attachment != 'None'
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96 #if $attachment_name == '':
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97 ent <- addFile(ent, galaxyClean("${attachment}"))
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98 #else
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99 ent <- addFile(ent, galaxyClean("${attachment}"), galaxyClean("${attachment_name}"))
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100 #end if
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101 #end if
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102
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103 ent <- storeEntity(ent)
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104
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105 write(properties(ent)\$id, file=galaxyClean("${outfile}"));
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106
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107 """
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108
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109
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110 import tempfile
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111 import os
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112 import sys
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113 import subprocess
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114
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115 h, path = tempfile.mkstemp()
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116 os.write(h,rcode)
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117 os.close(h)
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118
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119 proc = subprocess.Popen( ["Rscript", path] + sys.argv[1:], stderr=subprocess.PIPE, stdout=subprocess.PIPE )
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120 (stdoutdata, stderrdata) = proc.communicate()
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121 if proc.returncode:
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122 sys.stderr.write(stderrdata)
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123 sys.stdout.write(stdoutdata)
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124 os.unlink(path)
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125
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126 ]]></configfile>
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127 </configfiles>
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3
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128 <help>
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129
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130 Install R SynapseClient:
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131 source('http://depot.sagebase.org/CRAN.R')
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132 pkgInstall("synapseClient")
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133
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134 `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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135
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136 </help>
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137
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138 </tool> |
