Mercurial > repos > melissacline > ucsc_cancer_utilities

annotate segToMatrix.xml @ 58:3e5680fecd7a

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accept chr1 and 1
author jingchunzhu
date Tue, 22 Sep 2015 15:16:19 -0700
parents 2a240b005731
children bf57076e27b9
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1 <tool id="segToMatrix" name="segToMatrix" version="0.0.1">
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2 <description>
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3 Prepare segmented copy number data for Xena
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4 </description>
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5 <command interpreter="python">
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6 seg2matrix/segToMatrixGalaxy.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix $outputProbeMap $normal_CNV_value
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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" />
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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?">
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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 <param name="normal_CNV_value" type="text" value="0" lable="what is the value to represent normal copy number" />
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23 </inputs>
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24 <outputs>
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25 <data name="outputMatrix" format="tabular" label="xena copy number matrix" />
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26 <data name="outputProbeMap" format="tabular" label="associated probemap"/>
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27 </outputs>
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28 <help>
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30 **Given a segmented copy number data file, convert it into xena ready matrix file.**
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32 1. Input data file format: tab-deliminated
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34 ======= ===== ======= ===== ====== ======
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35 sample chr start end strand value
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36 ======= ===== ======= ===== ====== ======
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37 sample1 chr1 1 100 . 0.5
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38 sample2 chr1 101 1000 . 1.5
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39 sample3 chr1 1000 2000 . -0.5
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40 ... ... ... ... ... ...
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41 ======= ===== ======= ===== ====== ======
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44 2. Output File no 1. matrix file
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45
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46 Output File no 2. probeMap file -- probe to gene mapping file (is in the same genome assembly as the input segmented copy number data)
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47 </help>
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48 </tool>
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