Mercurial > repos > nicolas > oghma
changeset 13:377a34a001b0 draft
Uploaded
| author | nicolas |
|---|---|
| date | Fri, 21 Oct 2016 06:29:06 -0400 |
| parents | 87f772c49a20 |
| children | 4d21b6806e19 |
| files | qualityControl.xml |
| diffstat | 1 files changed, 41 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualityControl.xml Fri Oct 21 06:29:06 2016 -0400 @@ -0,0 +1,41 @@ +<tool id="qualityControl" name="qualityControl" version="1.0.0"> + <description>perform QC on a dataset</description> + <command interpreter="Rscript"> + qualityControl.R $config > ${reportPath} + </command> + + <inputs> + <param name="genotype" type="data" + label="genotype data" help="genotype must be a .csv" + /> + + <param name="plinkFreq" type="data" + label="plink files with frequencies" help="" + /> + + <param name="plinkHWE" type="data" + label="plink files with HardyWeinberg statistics" help="" + /> + </inputs> + + + <configfiles> + <configfile name="config"> +## Desc: this file is sourced in encode wrapper script +## as means to pass all galaxy params to R +"${genotype}" -> genotype +"${plinkFreq}" -> plinkFreq +"${plinkHWE}" -> plinkHWE +"${reportPath}" -> out + + </configfile> +</configfiles> + +<outputs> + <data format="plain text" name="reportPath" label="QC report" /> +</outputs> + + <help> + make a report with dimension of the dataset, MAF, Hardy-Weinberg test + </help> + </tool> \ No newline at end of file