Mercurial > repos > melissacline > ucsc_cancer_utilities

annotate segToMatrix.xml @ 37:e81019e3ac99

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Updated synapseGetDataset to look at the filename rather than the (no longer existant) content type field to determine if the data is in zip format
author melissacline
date Mon, 27 Jul 2015 16:29:24 -0700
parents 8e888e966c47
children 84eb11adc22f
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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 Prep 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 $input seg2matrix/$refGene.assembly $outputMatrix $outputProbeMap
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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 </inputs>
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23 <outputs>
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24 <data name="outputMatrix" format="tabular" label="xena copy number matrix" />
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25 <data name="outputProbeMap" format="tabular" label="associated probemap"/>
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26 </outputs>
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27 <help>
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28 ***Convert segmented copy number data for input into xena***
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29
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30 Given a segmented copy number data file, convert it into xena ready data files.
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32 File no 1. matrix file
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34 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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35 </help>
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36 </tool>
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