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1 <tool id="vl_import_data_object" name="VLI.data_object">
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2 <description>import DataObject definitions within omero/vl</description>
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3 <command interpreter="bash">
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4 launcher.sh
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5 --interpreter=python
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6 --runner=importer.py
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7 --host=$__user_omero_host__
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8 --user=$__user_omero_user__
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9 --passwd=$__user_omero_password__
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10 --operator=$__user_email__
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11 --ifile=${input}
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12 --ofile=${output}
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13 --report_file=${report}
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14 --logfile=${logfile}
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15 #if $blocking_validation
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16 --blocking-validator
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17 #end if
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18 data_object
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19 #if str($study) != 'use_provided'
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20 --study ${study}
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21 #end if
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22 #if str($mimetype) != 'use_provided'
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23 --mimetype=${mimetype}
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24 #end if
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25 </command>
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26
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27 <inputs>
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28 <param format="tabular" name="input" type="data"
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29 label="A tabular dataset with the following columns ..."/>
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30
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31 <param name="study" type="select" label="Context study" ajax = "True" ajax-source = "galaxy/get/studies" sort="True"
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32 help="Choose from the already defined studies. See below.">
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33 <option value="use_provided" selected="true">Records provide study labels</option>
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34 </param>
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35
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36 <param name="mimetype" type="select"
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37 label="mimetype for the data object."
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38 help="Choose from the following. See below.">
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39 <option value="use_provided" selected="true">
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40 Use record provided</option>
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41 <option value="x-vl/affymetrix-cel">x-vl/affymetrix-cel</option>
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42 </param>
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43
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44 <!-- ************************************************** -->
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45 <param name="blocking_validation" type="boolean" checked="false"
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46 label="Blocking validation"
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47 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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48
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49 <conditional name="wait_for_trigger">
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50 <param name="enable_trigger" type="boolean" checked="false"
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51 label="Wait for another tool to end before running this tool"/>
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52 <when value="true">
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53 <param format="txt" name="trigger_file" type="data"
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54 label="Select the LOG file that will be used as trigger"/>
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55 </when>
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56 </conditional>
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57
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58 </inputs>
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59
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60 <outputs>
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61 <data format="tabular" name="output" label="${tool.name}.mapping"/>
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62 <data format="tabular" name="report" label="${tool.name}.report"/>
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63 <data format="txt" name="logfile" label="${tool.name}.logfile"/>
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64 </outputs>
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65
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66 <stdio>
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67 <exit_code range="1:" level="fatal" />
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68 </stdio>
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69
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70 <help>
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71 Will read in a tsv file with the following columns::
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72
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73 study path data_sample mimetype size sha1
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74
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75 TEST01 file:/share/fs/v039303.cel V2902 x-vl/affymetrix-cel 39090 E909090
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76 ....
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77
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78 Records that point to an unknown data sample will be noisily
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79 ignored. The same will happen to records that have the same path of a
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80 previously seen data_object
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81 </help>
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82 </tool>
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