Mercurial > repos > melissacline > ucsc_cancer_utilities
changeset 32:8e888e966c47
change segToMatrix.xml location
| author | jingchunzhu |
|---|---|
| date | Fri, 24 Jul 2015 14:09:57 -0700 |
| parents | ab20c0d04f4a |
| children | ba042d3489c4 |
| files | seg2matrix/segToMatrix.xml segToMatrix.xml |
| diffstat | 2 files changed, 37 insertions(+), 36 deletions(-) [+] |
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--- a/seg2matrix/segToMatrix.xml Fri Jul 24 13:10:11 2015 -0700 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -<tool id="segToMatrix" name="segToMatrix" version="0.0.1"> - <description> - Prep segmented copy number data for Xena - </description> - <command interpreter="python"> - segToMatrixGalaxy.py $input $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> -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segToMatrix.xml Fri Jul 24 14:09:57 2015 -0700 @@ -0,0 +1,37 @@ +<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> +