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planemo upload commit 6139391ea037a297a151c74a909f089c26ac77e6
author rhpvorderman
date Wed, 18 Jan 2023 10:54:43 +0000
parents 264bc77bfed6
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ea681f34ca41 planemo upload commit 6139391ea037a297a151c74a909f089c26ac77e6
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1 <tool id="updio" name="UPDio" version="1.1.0+galaxy2" python_template_version="3.5" profile="21.05">
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2 <requirements>
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3 <requirement type="package" version="1.1.0">updio</requirement>
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4 <container type="docker">quay.io/biowdl/updio:1.1.0</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 ln -s $multisample_vcf input.vcf.gz &&
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8 updio --multisample_vcf input.vcf.gz
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9 --childID $child_id
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10 --momID $mom_id
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11 --dadID $dad_id &&
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12 mv output_dir/${child_id}.table ${updio_table} &&
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13 mv output_dir/${child_id}.upd ${updio_verdict}
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14 ]]></command>
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15 <inputs>
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16 <param name="multisample_vcf" type="data" format="vcf_bgzip"
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17 label="multisample VCF file" />
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18 <param name="child_id" type="text"
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19 label="child sample ID in the VCF file" />
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20 <param name="mom_id" type="text"
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21 label="Mother sample ID in the VCF file" />
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22 <param name="dad_id" type="text"
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23 label="Father sample ID in the VCF file" />
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24 </inputs>
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25 <outputs>
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26 <data format="tsv" name="updio_table" label="${tool.name} on ${child_id}: table"/>
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27 <data format="tsv" name="updio_verdict" label="${tool.name} on ${child_id}: verdict"/>
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28 </outputs>
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29 <help><![CDATA[
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30 UPDio is designed to detect UPD events in probands from vcf trio data.
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31 ]]></help>
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32 </tool>