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1 <tool id="vl_import_seq_data_sample" name="VLI.seq_data_sample">
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2 <description>
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3 Import sequencing related DataSample definitions within OMERO>biobank
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4 </description>
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5 <command interpreter="bash">
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6 launcher.sh
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7 --interpreter=python
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8 --runner=importer.py
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9 #if $omero_configuration.level == 'advanced'
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10 --host=$omero_configuration.vl_host
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11 --user=$omero_configuration.vl_user
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12 --passwd=$omero_configuration.vl_passwd
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13 #else
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14 --host=$__user_omero_host__
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15 --user=$__user_omero_user__
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16 --passwd=$__user_omero_password__
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17 #end if
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18 --operator=$__user_email__
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19 --ifile=${input}
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20 --ofile=${output}
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21 --report_file=${report}
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22 --logfile=${logfile}
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23 #if $blocking_validation
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24 --blocking-validator
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25 #end if
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26 seq_data_sample
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27 #if str($study) != 'use_provided'
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28 --study=${study}
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29 #end if
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30 #if str($source_type) != 'use_provided'
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31 --source-type=${source_type}
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32 #end if
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33 #if str($seq_dsample_type) != 'use_provided'
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34 --seq-dsample-type=${seq_dsample_type}
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35 #end if
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36 #if str($dsample_status) != 'use_provided'
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37 --status=${dsample_status}
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38 #end if
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39 #if str($device) != 'use_provided'
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40 --device=${device}
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41 #end if
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42 #if str($history) != 'None'
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43 --history=${history}
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44 #end if
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45 </command>
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46
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47 <inputs>
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48 <param format="tabular" name="input" type="data"
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49 label="A tabular dataset with the following columns..."/>
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50
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51 <param name="study" type="select" label="Context study" ajax = "True" ajax-source = "galaxy/get/studies" sort="True"
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52 help="Choose from the already defined studies. See below.">
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53 <option value="use_provided" selected="true">Records provide study labels</option>
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54 </param>
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55
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56 <param name="source_type" type="select"
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57 label="Type of the source"
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58 help="Choose from the following. See below.">
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59 <option value="use_provided" selected="true">
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60 Use record provided
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61 </option>
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62 <option value="FlowCell">FlowCell</option>
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63 <option value="SequencerOutput">
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64 SequencerOutput
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65 </option>
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66 <option value="RawSeqDataSample">
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67 RawSeqDataSample
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68 </option>
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69
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70 </param>
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71
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72 <!-- Choose the device after the type selection, SequencerOutput
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73 will required an HardwareDevice, RawSeqDataSample and SeqDataSample
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74 will required a SoftwareDevice. If the "use provided" is selected,
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75 load a generic Device select list -->
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76 <param name="seq_dsample_type" type="select"
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77 label="Type of the DataSample"
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78 help="Choose from the following. See below.">
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79 <option value="use_provided" selected="true">
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80 Use record provided
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81 </option>
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82 <option value="SequencerOutput">
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83 SequencerOutput
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84 </option>
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85 <option value="RawSeqDataSample">
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86 RawSeqDataSample
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87 </option>
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88 <option value="SeqDataSample">
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89 SeqDataSample
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90 </option>
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91 <option value="AlignedSeqDataSample">AlignedSeqDataSample</option>
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92 </param>
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93
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94 <param name="dsample_status" type="select" label="DataSample status" ajax = "True" ajax-source = "galaxy/get/data_sample_status" sort="True"
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95 help="Choose from one of the available values. See below.">
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96 <option value="use_provided" selected="true">Records provide status</option>
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97 </param>
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98
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99 <param name="device" type="select" label="device" ajax = "True" ajax-source = "galaxy/get/devices" sort="True"
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100 help="Choose from the already defined devices. See below.">
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101 <option value="use_provided" selected="true">Records provide device ids</option>
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102 </param>
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103
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104 <param format="txt" name="history" type="data" optional="true"
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105 label="Objects history"
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106 help="Galaxy history in JSON format, history will be shared among all objects"/>
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107
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108 <!-- ************************************************** -->
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109 <param name="blocking_validation" type="boolean" checked="false"
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110 label="Blocking validation"
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111 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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112
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113 <conditional name="wait_for_trigger">
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114 <param name="enable_trigger" type="boolean" checked="false"
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115 label="Wait for another tool to end before running this tool"/>
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116 <when value="true">
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117 <param format="txt" name="trigger_file" type="data"
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118 label="Select the LOG file that will be used as trigger"/>
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119 </when>
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120 </conditional>
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121
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122 <conditional name="omero_configuration">
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123 <param name="level" type="select" label="Configuration level">
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124 <option value="default" selected="true">Default: use Galaxy's preferences</option>
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125 <option value="advanced">Advanced: specify different host, user
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126 and password</option>
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127 </param>
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128 <when value="default"/>
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129 <when value="advanced">
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130 <param name="vl_host" size="40" type="text" value="hostname"
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131 label="OMERO.biobank host"/>
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132 <param name="vl_user" size="40" type="text" value="user"
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133 label="OMERO.biobank user"/>
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134 <param name="vl_passwd" size="40" type="text" value="password"
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135 label="OMERO.biobank passwd"/>
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136 </when>
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137 </conditional>
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138
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139 </inputs>
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140
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141 <outputs>
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142 <data format="tabular" name="output" label="${tool.name}.mapping"/>
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143 <data format="tabular" name="report" label="${tool.name}.report"/>
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144 <data format="txt" name="logfile" label="${tool.name}.logfile"/>
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145 </outputs>
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146
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147 <help>
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148 Will read a tsv file with the following columns::
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149
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150 study label source source_type seq_dsample_type status device
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151 FOOBAR seq_out_1 V012141 FlowCell SequencerOutput USABLE V123141
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152 FOOBAR seq_out_2 V012141 FlowCell SequencerOutput USABLE V123141
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153 FOOBAR seq_out_3 V1AD124 FlowCell SequencerOutput USABLE V123141
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154 ...
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155
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156 where
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157 * seq_dsample_type can assume one of the following values: SequencerOutput, RawSeqDataSample, SeqDataSample
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158 * source_type can assume one of the following values: FlowCell, SequencerOutput, RawSeqDataSample
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159
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160 study, source_type, seq_dsample_type, status and device columns can be
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161 overwritten by using command line options.
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162
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163 A special case of the previous file is when seq_dsample_type is
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164 SeqDataSample, in this case a mandatory sample column is required,
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165 this column has to contain IDs of Tube objects.
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166 The file will look like this
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167
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168 study label source source_type seq_dsample_type status device sample
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169 FOOBAR seq_dsample_1 V041241 SequencerOutput SeqDataSample USABLE VBB2351 V124AA41
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170 FOOBAR seq_dsample_2 V051561 SequencerOutput SeqDataSample USABLE VBB2351 V4151AAE
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171 FOOBAR seq_dsample_3 V151561 SequencerOutput SeqDataSample USABLE VBB2351 V15199CD
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172 ...
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173
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174 A file containing ax export of the Galaxy history that produced the
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175 data that are going to be imported can be passed as input parameter,
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176 history details must represented as a string serialized in JSON
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177 format.
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178 </help>
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179
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180 <stdio>
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181 <exit_code range="1:" level="fatal" />
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182 </stdio>
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183
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184 </tool>
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