Mercurial > repos > melissacline > ucsc_cancer_utilities
comparison segToGeneMatrix.xml @ 40:72dc9215623d
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| author | jingchunzhu |
|---|---|
| date | Fri, 31 Jul 2015 21:29:17 -0700 |
| parents | 61f03b481b0d |
| children | 728eda331f07 |
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| 39:61f03b481b0d | 40:72dc9215623d |
|---|---|
| 1 <tool id="segToGeneMatrix" name="segToGeneMatrix" version="0.0.1"> | 1 <tool id="segToGeneMatrix" name="segToGeneMatrix" version="0.0.1"> |
| 2 <description> | 2 <description> |
| 3 Convert segmented copy number data to gene based matrix data | 3 Convert segmented copy number data to gene-level matrix data |
| 4 </description> | 4 </description> |
| 5 <command interpreter="python"> | 5 <command interpreter="python"> |
| 6 seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix | 6 seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix |
| 7 </command> | 7 </command> |
| 8 <inputs> | 8 <inputs> |
| 22 </inputs> | 22 </inputs> |
| 23 <outputs> | 23 <outputs> |
| 24 <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" /> | 24 <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" /> |
| 25 </outputs> | 25 </outputs> |
| 26 <help> | 26 <help> |
| 27 ***Convert segmented copy number data for input into xena*** | |
| 28 | 27 |
| 29 Given a segmented copy number data file, convert it into gene based matrix data | 28 **Given a segmented copy number data file, convert it into gene-level matrix data, also xena ready** |
| 30 | 29 |
| 31 Output File no 1. matrix file | 30 Output File no 1. matrix file |
| 32 | 31 |
| 33 </help> | 32 </help> |
| 34 </tool> | 33 </tool> |