view galaxy-tools/biobank/utils/prepare_seq_out_inputs.xml @ 0:ba6cf6ede027 draft default tip

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<tool id="vl_prepare_seq_out_inputs"
      name="VLUTIL.prepare_seq_out_inputs">
  <description>
    Extract OMERO.biobank objects that can be used to import SequencerOutput data
  </description>

 <command interpreter="bash">
    launcher.sh
    --interpreter=python
    --runner=prepare_seq_out_inputs.py
    --in-file=${infile}
    --logfile=${log_file}
    --dsamples-out-file=${dsamples_ofile}
    --dobjects-out-file=${dobjects_ofile}
    --study=${study}
  </comand>

  <inputs>
    <param format="tabular" name="infile" type="data"
      label="Input file (in TAB-separated format)"/>
    <param name="study" size="40" type="text" label="Study label"/>
  </inputs>

  <outputs>
    <data format="tabular" name="dsamples_ofile"
      label="${tool.name}_dsamples.tsv"/>
    <data format="tabular" name="dobjects_ofile"
      label="${tool.name}_dobjects.tsv"/>
    <data format="txt" name="log_file"
      label="${tool.name}.log"/>
  </outputs>

  <help>
This tool produces files that can be used as input to import
 * SequencerOutput data samples
 * SequencerOutput data objects
within OMERO.biobank using import applications.

Input file must be like

 run_directory                   path
 130418_SN194_0303_BC1NYHACXX    file:///SHARE/USERFS/els7/users/sequencing_data/completed/130418_SN194_0303_BC1NYHACXX/raw
 160418_SN194_0304_BCAZYHACXX    file:///SHARE/USERFS/els7/users/sequencing_data/completed/160418_SN194_0304_BCAZYHACXX/raw
 ....
  </help>
</tool>