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1 <tool id="vl_import_biosample" name="VLI.biosample">
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2 <description>import BioSample definitions within omero/vl</description>
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3 <command interpreter="python">
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4 #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py
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5 #else #unauthorized_access.py
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6 #end if
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7 #if $advanced_configuration.configuration_level == 'advanced'
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8 --host=$advanced_configuration.vl_host
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9 --user=$advanced_configuration.vl_user
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10 --passwd=$advanced_configuration.vl_passwd
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11 #end if
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12 --operator=galaxy
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13 --ifile=${input}
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14 --ofile=${output}
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15 --report_file=${report}
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16 --loglevel=$__app__.config.vl_loglevel
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17 --logfile=${logfile}
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18 #if $blocking_validation
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19 --blocking-validator
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20 #end if
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21 biosample
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22 #if str($study) != 'use_provided'
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23 --study ${study}
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24 #end if
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25 #if str($source_type) != 'use_provided'
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26 --source-type ${source_type}
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27 #end if
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28 #if str($vessel_type_selector.vessel_type) != 'use_provided'
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29 --vessel-type ${vessel_type_selector.vessel_type}
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30 #end if
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31 #if str($vessel_content) != 'use_provided'
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32 --vessel-content=${vessel_content}
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33 #end if
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34 #if str($vessel_status) != 'use_provided'
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35 --vessel-status=${vessel_status}
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36 #end if
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37 #if str($vessel_type_selector) == 'IlluminaBeadChipArray'
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38 #if str($vessel_type_selector.assay_type) != 'use_provided'
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39 --bead-chip-assay-type=${vessel_type_selector.assay_type}
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40 #end if
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41 #end if
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42 </command>
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43
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44 <inputs>
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45 <param format="tabular" name="input" type="data"
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46 label="A tabular dataset with the following columns ..."/>
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47
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48 <param name="study" type="select" label="Context study"
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49 help="Choose from the already defined studies. See below.">
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50 <options from_parameter="tool.app.known_studies"
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51 transform_lines="[ "%s%s%s:%s"
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52 % ( l[0], self.separator, l[0], l[1][:40] )
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53 for l in obj ]">
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54 <column name="value" index="0"/>
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55 <column name="name" index="1"/>
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56 <filter type="sort_by" column="0"/>
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57 <filter type="add_value" name="Records provide study labels"
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58 value="use_provided" index="0"/>
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59 </options>
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60 </param>
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61
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62 <param name="source_type" type="select"
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63 label="type of the source object"
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64 help="Choose from the legal types. See below.">
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65 <option value="use_provided" selected="true">
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66 Use what provided by record</option>
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67 <option value="Tube">Tube</option>
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68 <option value="PlateWell">PlateWell</option>
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69 <option value="Individual">Individual</option>
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70 <option value="NO_SOURCE">No source provided</option>
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71 </param>
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72
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73 <conditional name="vessel_type_selector">
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74 <param name="vessel_type" type="select"
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75 label="type of the vessel object"
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76 help="Choose from the legal types. See below.">
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77 <option value="use_provided" selected="true">
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78 Use what provided by record
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79 </option>
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80 <option value="Tube">Tube</option>
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81 <option value="PlateWell">PlateWell</option>
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82 <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option>
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83 </param>
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84 <when value="IlluminaBeadChipArray">
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85 <param name="assay_type" type="select" label="Illumina Bead Chip Array Assay type"
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86 help="Choose from the following assay types">
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87 <options from_parameter="tool.app.known_illumina_beadchip_assay_type"
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88 transform_lines="[ "%s%s%s"
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89 % (o[1], self.separator, o[1])
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90 for o in obj ]">
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91 <column name="value" index="0"/>
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92 <column name="name" index="1"/>
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93 <filter type="sort_by" column="0"/>
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94 <filter type="add_value" name="Records provide assay type"
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95 value="use_provided" index="0"/>
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96 </options>
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97 </param>
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98 </when>
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99 </conditional>
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100
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101 <param name="vessel_content" type="select" label="Vessel content"
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102 help="Choose from one of the available values. See below.">
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103 <options from_parameter="tool.app.kb.VesselContent.__enums__"
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104 transform_lines="[ "%s%s%s"
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105 % (e.enum_label(),
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106 self.separator,
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107 e.enum_label())
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108 for e in obj ]">
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109 <column name="value" index="0"/>
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110 <column name="name" index="1"/>
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111 <filter type="sort_by" column="0"/>
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112 <filter type="add_value" name="Records provide vessel content"
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113 value="use_provided" index="0"/>
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114 </options>
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115 </param>
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116 <param name="vessel_status" type="select" label="Vessel status"
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117 help="Choose from one of the available values. See below.">
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118 <options from_parameter="tool.app.kb.VesselStatus.__enums__"
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119 transform_lines="[ "%s%s%s"
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120 % (e.enum_label(),
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121 self.separator,
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122 e.enum_label())
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123 for e in obj ]">
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124 <column name="value" index="0"/>
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125 <column name="name" index="1"/>
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126 <filter type="sort_by" column="0"/>
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127 <filter type="add_value" name="Records provide vessel status"
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128 value="use_provided" index="0"/>
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129 </options>
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130 </param>
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131
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132 <conditional name="extra_fields">
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133 <param name="enabled" type="select"
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134 label="Enable extra optional fields">
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135 <option value="no" selected="true">no</option>
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136 <option value="yes">yes</option>
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137 </param>
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138 <when value="no"/>
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139 <when value="yes">
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140 <param name="current_volume" type="float"
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141 value="20"
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142 help="fluid (FIXME UNITS) currently held in the vessel">
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143 <validator type="in_range" message="Volume must be positive"
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144 min="0" max="inf"/>
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145 </param>
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146 <param name="used_volume" type="float"
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147 value="20"
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148 help="amount of source fluid (FIXME UNITS) used">
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149 <validator type="in_range" message="Volume must be positive"
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150 min="0" max="inf"/>
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151 </param>
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152 </when>
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153 </conditional>
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154
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155 <!-- ************************************************** -->
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156 <param name="blocking_validation" type="boolean" checked="false"
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157 label="Blocking validation"
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158 help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/>
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159
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160 <conditional name="wait_for_trigger">
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161 <param name="enable_trigger" type="boolean" checked="false"
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162 label="Wait for another tool to end before running this tool"/>
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163 <when value="true">
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164 <param format="txt" name="trigger_file" type="data"
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165 label="Select the LOG file that will be used as trigger"/>
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166 </when>
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167 </conditional>
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168
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169 <conditional name="advanced_configuration">
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170 <param name="configuration_level" type="select"
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171 label="Configuration level">
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172 <option value="default" selected="true">Default configuration</option>
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173 <option value="advanced">Advanced configuration</option>
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174 </param>
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175 <when value="default"/>
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176 <when value="advanced">
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177 <param name="vl_host" size="40" type="text" value="localhost"
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178 label="Omero/VL host"/>
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179 <param name="vl_user" size="20" type="text" value="root"
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180 label="Omero/VL user"/>
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181 <param name="vl_passwd" size="20" type="text" value="What? Me_worry?"
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182 label="Omero/VL passwd"/>
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183 </when>
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184 </conditional>
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185 </inputs>
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186
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187 <outputs>
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188 <data format="tabular" name="output" label="${tool.name}.mapping"/>
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189 <data format="tabular" name="report" label="${tool.name}.report"/>
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190 <data format="txt" name="logfile" label="${tool.name}.logfile"/>
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191 </outputs>
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192
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193 <help>
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194 A biosample record will have, at least, the following fields::
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195
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196 label source
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197 I001-bs-2 V932814892
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198 I002-bs-2 V932814892
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199 I003-bs-2 None
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200
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201 Where label is the label of the biosample container. If a 'None' value
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202 has been passed in the source column, the biosample will be imported
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203 as a new unlinked object into the biobanks. Another example, this time
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204 involving DNA samples::
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205
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206 label source used_volume current_volume activation_date
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207 I001-dna V932814899 0.3 0.2 17/03/2007
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208 I002-dna V932814900 0.22 0.2 21/01/2004
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209
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210 A special case is when records refer to biosamples contained in plate
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211 wells. In this case, an additional column must be present with the VID
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212 of the corresponding TiterPlate object. For instance::
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213
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214 plate label source
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215 V39030 A01 V932814892
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216 V39031 A02 V932814893
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217 V39032 A03 V932814894
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218
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219 where the label column is now the label of the well position.
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220
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221 If row and column (optional) are provided, the program will use them;
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222 if they are not provided, it will infer them from label (e.g., J01 ->
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223 row=10, column=1). Missing labels will be generated as::
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224
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225 '%s%03d' % (chr(row+ord('A')-1), column)
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226
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227 A badly formed label will result in the rejection of the record; the
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228 same will happen if label, row and column are inconsistent. The well
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229 will be filled by current_volume material produced by removing
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230 used_volume material taken from the bio material contained in the
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231 vessel identified by source. row and column are base 1.
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232
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233 If the sample is a IlluminaBeadChipArray the plate column used in the
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234 PlateWell case will become a illumina_array column and a new column, named
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235 bead_chip_assay_type, is required::
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236
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237 illumina_array label source bead_chip_assay_type
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238 V1351235 R01C01 V412441 HUMANEXOME_12V1_B
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239 V1351235 R01C02 V351151 HUMANEXOME_12V1_B
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240 V1351235 R02C01 V345115 HUMANEXOME_12V1_B
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241 </help>
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242
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243 <stdio>
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244 <exit_code range="1:" level="fatal" />
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245 </stdio>
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246
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247 </tool>
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