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1 <tool id="segToGeneMatrix" name="segToGeneMatrix" version="0.0.1">
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2 <description>
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3 Convert segmented copy number data to gene-level matrix data
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4 </description>
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5 <command interpreter="python">
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6 seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix
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7 </command>
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8 <inputs>
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9 <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" help="See input data format section for required input format" />
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10 <conditional name="refGene">
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11 <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?" help="Copy number segments will be map to RefGenes of the selected assembly.">
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12 <option value="hg19">hg19</option>
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13 <option value="hg18">hg18</option>
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14 </param>
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15 <when value="hg19">
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16 <param name="assembly" type="hidden" value="refGene_hg19" />
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17 </when>
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18 <when value="hg18">
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19 <param name="assembly" type="hidden" value="refGene_hg18" />
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20 </when>
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21 </conditional>
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22 </inputs>
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23 <outputs>
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24 <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" />
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25 </outputs>
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26 <help>
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27
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28 **Given a segmented copy number data file, convert it into gene-level matrix data, also xena ready**
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29
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30 1. Input data file format: tab-deliminated
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31
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32 ======= ===== ======= ===== ====== ======
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33 sanmple chr start end strand value
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34 ======= ===== ======= ===== ====== ======
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35 sample1 chr1 1 100 . 0.5
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36 sample2 chr1 101 1000 . 1.5
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37 sample3 chr1 1000 2000 . -0.5
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38 ... ... ... ... ... ...
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39 ======= ===== ======= ===== ====== ======
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40
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41
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42 2. Output file: gene-level matrix file
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43
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44 </help>
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45 </tool>
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46
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