Mercurial > repos > melissacline > ucsc_cancer_utilities
comparison segToGeneMatrix.xml @ 54:59dbe857f5d4
introduce normal_CNV parameter
| author | jingchunzhu |
|---|---|
| date | Thu, 17 Sep 2015 22:03:04 -0700 |
| parents | 728eda331f07 |
| children | 2a240b005731 |
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| 53:7de3db823f90 | 54:59dbe857f5d4 |
|---|---|
| 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-level 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 $normal_CNV_value |
| 7 </command> | 7 </command> |
| 8 <inputs> | 8 <inputs> |
| 9 <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" /> | 9 <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" /> |
| 10 <conditional name="refGene"> | 10 <conditional name="refGene"> |
| 11 <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."> | 11 <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."> |
| 16 <param name="assembly" type="hidden" value="refGene_hg19" /> | 16 <param name="assembly" type="hidden" value="refGene_hg19" /> |
| 17 </when> | 17 </when> |
| 18 <when value="hg18"> | 18 <when value="hg18"> |
| 19 <param name="assembly" type="hidden" value="refGene_hg18" /> | 19 <param name="assembly" type="hidden" value="refGene_hg18" /> |
| 20 </when> | 20 </when> |
| 21 </conditional> | 21 </conditional> |
| 22 <param name="normal_CNV_value" type="text" value="0" lable="what is the value to represent normal copy number" /> | |
| 22 </inputs> | 23 </inputs> |
| 23 <outputs> | 24 <outputs> |
| 24 <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" /> | 25 <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" /> |
| 25 </outputs> | 26 </outputs> |
| 26 <help> | 27 <help> |