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1 <tool id="extract_TCGA_survival_data" name="Extract TCGA Survival Data" force_history_refresh="True">
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2 <command interpreter="python">extract.TCGA.survival.data.py
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3 -d $dataset
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4 -o ${output}
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5
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6 </command>
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7 <inputs>
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8 <param name="dataset" type="data" format='tabular' label="Raw Clinical Data"/>
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9 </inputs>
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10 <outputs>
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11 <data format="tabular" name="output" label="Formatted Clinical Data"/>
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12 </outputs>
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13 <help>
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14 .. class:: infomark
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15
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16 **Format Raw TCGA Clinical Data** - Tool to convert a raw clinical TCGA data file into a the format expected by the Survival Analysis tools
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17
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18 **OUTPUT:** A new clinical data file that is a 2 column, tab-delimited file of the format that is expected by the Survival Analysis tools
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19
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20 </help>
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21 </tool>
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