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1 <tool id="split_by_study"
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2 name="VLUTIL.split_individuals_by_study"
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3 force_history_refresh="true">
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4
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5 <description>
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6 Split a file containing pedigree informations in multiple files using the study as split criteria
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7 </description>
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8
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9 <command interpreter="bash">
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10 launcher.sh
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11 --interpreter=python
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12 --runner=split_by_study.py
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13 --in-file=${in_file}
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14 --logfile=${log_file}
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15 --record-id=$log_file.id
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16 --out-path=$__new_file_path__
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17 </command>
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18
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19 <inputs>
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20 <param format="tabular" name="in_file" type="data"
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21 label="input TSV file"/>
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22 </inputs>
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23
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24 <outputs>
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25 <data format="txt" name="log_file"
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26 label="${tool.name}.log"/>
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27 </outputs>
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28
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29 <help>
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30 Split a file like::
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31
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32 individual gender father mother
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33 ASTUDY:2141 MALE ASTUDY:12 ASTUDY:12341
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34 ASTUDY:415 MALE ASTUDY:3562 ASTUDY:13612
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35 BSTUDY:12515 FEMALE BSTUDY:3512 BSTUDY:124
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36
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37 into multiple files based on the STUDY value of the label stored in the "individual" column.
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38 Each label in the "individual" column must have a STUDY:ENROLLMENT_CODE format, otherwise the line
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39 will be skipped.
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40 </help>
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41
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42 </tool> |
