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1 <tool id="run_all" name="PathOGiST - Run All" version="1.0.0">
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2 <description>: Runs the entire PathOGiST pipeline</description>
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3 <requirements>
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4 <requirement type="package" version="0.3">pathogist</requirement>
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5 </requirements>
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6
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7 <command><![CDATA[
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8 PATHOGIST $config
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9 ]]></command>
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10
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11 <inputs>
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12 <param name="config" type="data" format="yaml" label="Config YAML"
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13 help="Config YAML file for PathOGiST"/>
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14 </inputs>
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15
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16 <outputs>
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17 <data name="clustering" label="Consensus clustering on ${on_string}" format="tabular" from_work_dir="cc.tsv"/>
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18 </outputs>
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19
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20 <help>
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21
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22 </help>
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23
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24 <citations>
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25
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26 </citations>
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27 </tool>
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