Mercurial > repos > melissacline > ucsc_cancer_utilities
comparison segToMatrix.xml @ 54:59dbe857f5d4
introduce normal_CNV parameter
| author | jingchunzhu |
|---|---|
| date | Thu, 17 Sep 2015 22:03:04 -0700 |
| parents | 3a036a34c362 |
| children | 2a240b005731 |
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| 53:7de3db823f90 | 54:59dbe857f5d4 |
|---|---|
| 1 <tool id="segToMatrix" name="segToMatrix" version="0.0.1"> | 1 <tool id="segToMatrix" name="segToMatrix" version="0.0.1"> |
| 2 <description> | 2 <description> |
| 3 Prepare segmented copy number data for Xena | 3 Prepare segmented copy number data for Xena |
| 4 </description> | 4 </description> |
| 5 <command interpreter="python"> | 5 <command interpreter="python"> |
| 6 seg2matrix/segToMatrixGalaxy.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix $outputProbeMap | 6 seg2matrix/segToMatrixGalaxy.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix $outputProbeMap $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" /> | 9 <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" /> |
| 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?"> | 11 <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?"> |
| 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="xena copy number matrix" /> | 25 <data name="outputMatrix" format="tabular" label="xena copy number matrix" /> |
| 25 <data name="outputProbeMap" format="tabular" label="associated probemap"/> | 26 <data name="outputProbeMap" format="tabular" label="associated probemap"/> |
| 26 </outputs> | 27 </outputs> |