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

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<tool id="vl_prepare_seq_dsample_inputs" 
      name="VLUTIL.prepare_seq_dsample_inputs">
  <description>
    Extract OMERO.biobank objects from a sequencing samplesheet
  </description>

  <command interpreter="bash">
    launcher.sh
    --interpreter=python
    --runner=prepare_seq_dsample_inputs.py
    --in-file=${infile}
    --logfile=${log_file}
    --tubes-out-file=${tubes_ofile}
    --flowcells-out-file=${flowcells_ofile}
    --lanes-out-file=${lanes_ofile}
    --laneslots-out-file=${laneslots_ofile}
    --config-parameters=${config_params}
    --study-output-file=${study_ofile}
    --tubes-subsamples-output-file=${subsamples_ofile}
  </command>

  <inputs>
    <param format="tabular" name="infile" type="data"
	   label="Sampelsheet (in TAB-separated format)"/>
    <param format="txt" name="config_params" type="data"
	   label="Configuration parameters" optional="false"/>
  </inputs>

  <outputs>
    <data format="tabular" name="tubes_ofile"
	  label="${tool.name}_tubes.tsv"/>
    <data format="tabular" name="subsamples_ofile"
	  label="${tool.name}_subsamples.tsv"/>
    <data format="tabular" name="flowcells_ofile"
	  label="${tool.name}_flowcells.tsv"/>
    <data format="tabular" name="lanes_ofile"
	  label="${tool.name}_lanes.tsv"/>
    <data format="tabular" name="laneslots_ofile"
	  label="${tool.name}_laneslots.tsv"/>
    <data format="tabular" name="study_ofile"
	  label="${tool.name}_study.tsv"/>
    <data format="txt" name="log_file"
	  label="${tool.name}.log"/>
  </outputs>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>

  <help>
This tool produces files that can be used as input to import
 * samples
 * flowcells
 * lanes
 * laneslots

within OMERO.biobank using import applications.

If the optional 'study-output-file' parameter is given as input, the
script will produce the input file for a new study definition.

If the optional 'tubes-subsamples-output-file' is given, the script
will generate another file with tubes definitions where each tube is
produced appliying a specific laboratory protocol to an existing
tube. Existing tubes are the ones in tubes-out-file, new tubes' labels
are created using the pattern **tube_label::protocol**
The config_parameters field must point to a YAML configuration file
with the following structure:

  config_parameters:
    study_label: study_label
    
    namespace: namespace

where study_label is mandatory
  </help>
</tool>