Mercurial > repos > melissacline > ucsc_cancer_utilities
view segToGeneMatrix.xml @ 52:3a036a34c362
better handle of input file
author | jingchunzhu |
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date | Thu, 17 Sep 2015 15:00:45 -0700 |
parents | 728eda331f07 |
children | 59dbe857f5d4 |
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<tool id="segToGeneMatrix" name="segToGeneMatrix" version="0.0.1"> <description> Convert segmented copy number data to gene-level matrix data </description> <command interpreter="python"> seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix </command> <inputs> <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" /> <conditional name="refGene"> <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."> <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="gene-level copy number matrix" /> </outputs> <help> **Given a segmented copy number data file, convert it into gene-level matrix data, also xena ready** 1. Input data file format: tab-deliminated ======= ===== ======= ===== ====== ====== sanmple chr start end strand value ======= ===== ======= ===== ====== ====== sample1 chr1 1 100 . 0.5 sample2 chr1 101 1000 . 1.5 sample3 chr1 1000 2000 . -0.5 ... ... ... ... ... ... ======= ===== ======= ===== ====== ====== 2. Output file: gene-level matrix file </help> </tool>