Mercurial > repos > melissacline > ucsc_cancer_utilities
view segToMatrix.xml @ 36:ab161b5ac9cc
Removing the dependency on synapseclient version, testing that...
author | melissacline |
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date | Mon, 27 Jul 2015 15:55:22 -0700 |
parents | 8e888e966c47 |
children | 84eb11adc22f |
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<tool id="segToMatrix" name="segToMatrix" version="0.0.1"> <description> Prep segmented copy number data for Xena </description> <command interpreter="python"> seg2matrix/segToMatrixGalaxy.py $input seg2matrix/$refGene.assembly $outputMatrix $outputProbeMap </command> <inputs> <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" /> <conditional name="refGene"> <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?"> <option value="hg19">hg19</option> <option value="hg18">hg18</option> </param> <when value="hg19"> <param name="assembly" type="hidden" value="refGene_hg19" /> </when> <when value="hg18"> <param name="assembly" type="hidden" value="refGene_hg18" /> </when> </conditional> </inputs> <outputs> <data name="outputMatrix" format="tabular" label="xena copy number matrix" /> <data name="outputProbeMap" format="tabular" label="associated probemap"/> </outputs> <help> ***Convert segmented copy number data for input into xena*** Given a segmented copy number data file, convert it into xena ready data files. File no 1. matrix file File no 2. probeMap file -- probe to gene mapping file (is in the same genome assembly as the input segmented copy number data) </help> </tool>