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1 <tool id="vl_prepare_seq_dsample_inputs"
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2 name="VLUTIL.prepare_seq_dsample_inputs">
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3 <description>
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4 Extract OMERO.biobank objects from a sequencing samplesheet
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5 </description>
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6
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7 <command interpreter="python">
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8 prepare_seq_dsample_inputs.py
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9 --in-file=${infile}
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10 --loglevel=$__app__.config.vl_loglevel
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11 --logfile=${log_file}
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12 --tubes-out-file=${tubes_ofile}
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13 --flowcells-out-file=${flowcells_ofile}
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14 --lanes-out-file=${lanes_ofile}
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15 --laneslots-out-file=${laneslots_ofile}
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16 --config-parameters=${config_params}
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17 --study-output-file=${study_ofile}
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18 --tubes-subsamples-output-file=${subsamples_ofile}
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19 </command>
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20
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21 <inputs>
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22 <param format="tabular" name="infile" type="data"
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23 label="Samplesheet (in TAB-separated format)"/>
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24 <param format="txt" name="config_params" type="data"
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25 label="Configuration parameters" optional="false"/>
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26 </inputs>
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27
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28 <outputs>
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29 <data format="tabular" name="tubes_ofile"
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30 label="${tool.name}_tubes.tsv"/>
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31 <data format="tabular" name="subsamples_ofile"
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32 label="${tool.name}_subsamples.tsv"/>
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33 <data format="tabular" name="flowcells_ofile"
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34 label="${tool.name}_flowcells.tsv"/>
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35 <data format="tabular" name="lanes_ofile"
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36 label="${tool.name}_lanes.tsv"/>
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37 <data format="tabular" name="laneslots_ofile"
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38 label="${tool.name}_laneslots.tsv"/>
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39 <data format="tabular" name="study_ofile"
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40 label="${tool.name}_study.tsv"/>
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41 <data format="txt" name="log_file"
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42 label="${tool.name}.log"/>
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43 </outputs>
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44
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45 <stdio>
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46 <exit_code range="1:" level="fatal" />
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47 </stdio>
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48
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49 <help>
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50 This tool produces files that can be used as input to import
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51 * samples
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52 * flowcells
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53 * lanes
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54 * laneslots
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55
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56 within OMERO.biobank using import applications.
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57
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58 If the optional 'study-output-file' parameter is given as input, the
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59 script will produce the input file for a new study definition.
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60
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61 If the optional 'tubes-subsamples-output-file' is given, the script
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62 will generate another file with tubes definitions where each tube is
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63 produced appliying a specific laboratory protocol to an existing
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64 tube. Existing tubes are the ones in tubes-out-file, new tubes' labels
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65 are created using the pattern **tube_label::protocol**
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66 The config_parameters field must point to a YAML configuration file
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67 with the following structure:
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68
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69 config_parameters:
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70 study_label: study_label
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71
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72 namespace: namespace
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73
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74 where study_label is mandatory
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75 </help>
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76 </tool>
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