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1 <tool id="fix_and_merge_TCGA_samples_IDs" name="Fix and Merge TCGA sample IDs" force_history_refresh="True">
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2 <command interpreter="python">fix.and.merge.TCGA.sample.IDs.py
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3 -d $dataset -n ${num_components} ${remove_normals}
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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="Matrix with Full TCGA Aliquot Barcodes"/>
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9 <param name="num_components" type="integer" label="Number of barcode components to use (min number is 3)" value="3" />
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10 <param name="remove_normals" type="boolean" label="Remove Normals from Matrix? (check to exclude)" truevalue="-r" falsevalue="" checked="True" />
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="output" label="Matrix with TCGA Patient Barcodes (filtered and merged)"/>
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14 </outputs>
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15 <help>
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16 .. class:: infomark
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17
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18 **Update and Merge TCGA Sample IDs** - This will limit the TCGA sample IDs to the specified numnber of elements (min is 3). If necessary, samples will be merged (by averaging)
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19
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20 **OUTPUT:** A new matrix using sample (columns) that use the specified number of components
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21
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22 ----
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23
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24 **Parameters**
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25
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26 - **Matrix with TCGA barcode sample IDs (e.g. TCGA-AE-####-01-)** Specify a data matrix with TCGA barcodes
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27
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28 - **Number of barcode components to use** Specify the number of barcode components to use in new matrix that is produced **(min number is 3)**
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29
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30 - **Remove Normals from Matrix?** - Remove any normals from the matrix (if necessary)
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31
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32 </help>
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33 </tool>
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