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1 <tool id="remove_tcga_normal_samples" name="Remove TGCA Normal Samples" force_history_refresh="True">
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2 <command interpreter="python">remove.tcga.normals.py
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3 -d $dataset
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4 -o ${output_tumor}
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5 -r ${return_normal_matrix}
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6 #if str($return_normal_matrix) == 'yes':
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7 -O ${output_normal}
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8 #end if
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9 </command>
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10 <inputs>
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11 <param name="dataset" type="data" format='tabular' label="Matrix containing TCGA Normal Samples"/>
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12 <param name="return_normal_matrix" type='select' display="radio" label="Return Normals in Separate File?" help="Specify whether or not to return a file containing the normals">
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13 <option value="yes" selected='true' >Yes</option>
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14 <option value="no">No</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="output_tumor" label="Tumor Sample Matrix"/>
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19 <data format="tabular" name="output_normal" label="Normal Sample Matrix">
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20 <filter>(return_normal_matrix)=="yes"</filter>
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21 </data>
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22 </outputs>
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23 <help>
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24 .. class:: infomark
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25
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26 **Remove Normal Samples** - Tool to remove the normal samples from a matrix **(ASSUMES samples are in the columns of matrix)**
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27
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28 **OUTPUT:** A new matrix without normal samples
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29
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30 ----
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31
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32 **INPUT**
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33
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34 - **Matrix that contains normal samples** Input matrix that potentially contains normal samples
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35
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36
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37 </help>
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38 </tool>
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