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1 <tool id="mergeMutationDatasets" description="Merge two Xena positional mutation datasets into a new dataset" name="Merge Xena Mutation by Position Data" version="0.0.1">
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19
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2 <command interpreter="python">
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3 mergeXenaMutation.py $outputC $outputSourceMatrix $errorLog $inputA $inputB
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4 #if $labelForDatasetA
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5 --aLabel "${labelForDatasetA}"
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41
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6 #else
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7 --aLabel "${inputA.name}"
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8 #end if
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9 #if $labelForDatasetB
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10 --bLabel "${labelForDatasetB}"
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41
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11 #else
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12 --bLabel "${inputB.name}"
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19
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13 #end if
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14 </command>
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15 <inputs>
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16 <param name="inputA" format="tabular" type="data" label="Xena Mutation by Position Dataset A"/>
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17 <param type="text" name="labelForDatasetA" label="Dataset A Label (eg. LGG)" value="A"/>
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18 <param name="inputB" format="tabular" type="data" label="Xena Mutation by Position Dataset B"/>
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19 <param type="text" name="labelForDatasetB" label="Dataset B Label (eg. GBM)" value="B"/>
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19
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20 </inputs>
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21 <outputs>
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22 <data name="errorLog" format="data" label="Execution Log" hidden="True" />
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23 <data name="outputSourceMatrix" format="tabular" label="Data Source ${labelForDatasetA}+${labelForDatasetB}"/>
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24 <data name="outputC" format="tabular" label="Mutation by Position ${labelForDatasetA}+${labelForDatasetB}"/>
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19
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25 </outputs>
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26 <help>
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27
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56
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28 **Merge Xena Positional Mutation Datasets**
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29
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30 1. Input xena positional mutation data file format: tab-deliminated
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31
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32 ======= ===== ======= ===== ========= ====== ========
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33 sample chr start end reference alt anything
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34 ======= ===== ======= ===== ========= ====== ========
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35 sample1 chr1 1 1 A T 0.2
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36 sample1 chr1 10 10 T A 0.1
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37 sample2 chr1 20 20 G GG 0.0
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38 sample2 chr1 20 21 GT G
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39 ... ... ... ... ... ... ...
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40 ======= ===== ======= ===== ========= ====== ========
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41
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42
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43 2. Output file 1: Given two datasets of mutation data, merge them to produce a third dataset that is the union of the first two. The new dataset will contain all mutations from either dataset.
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44
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45 3. Output file 2: To maintain provenance, this script also outputs a second data file, with one row for each sample ID that appears in the output dataset, and two columns per row indicating which input dataset(s) contained some mutation data for that sample. Users can specify descriptive labels to indicate the data source. </help>
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46 </tool>
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