comparison galaxy-tools/biobank/utils/split_by_study.xml @ 0:ba6cf6ede027 draft default tip

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0:ba6cf6ede027

<tool id="split_by_study"
      name="VLUTIL.split_individuals_by_study"
      force_history_refresh="true">

    <description>
        Split a file containing pedigree informations in multiple files using the study as split criteria
    </description>

    <command interpreter="bash">
        launcher.sh
        --interpreter=python
        --runner=split_by_study.py
        --in-file=${in_file}
        --logfile=${log_file}
        --record-id=$log_file.id
        --out-path=$__new_file_path__
    </command>

    <inputs>
        <param format="tabular" name="in_file" type="data"
               label="input TSV file"/>
    </inputs>

    <outputs>
        <data format="txt" name="log_file"
              label="${tool.name}.log"/>
    </outputs>

    <help>
Split a file like::

  individual    gender  father       mother
  ASTUDY:2141   MALE    ASTUDY:12    ASTUDY:12341
  ASTUDY:415    MALE    ASTUDY:3562  ASTUDY:13612
  BSTUDY:12515  FEMALE  BSTUDY:3512  BSTUDY:124

into multiple files based on the STUDY value of the label stored in the "individual" column.
Each label in the "individual" column must have a STUDY:ENROLLMENT_CODE format, otherwise the line
will be skipped.
    </help>

</tool>