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GRsetFromGEO/GRsetFromGEO.xml |
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| diff -r c356d89b0145 -r dc0d9276a8f1 GRsetFromGEO/GRsetFromGEO.xml --- a/GRsetFromGEO/GRsetFromGEO.xml Mon Aug 21 06:28:18 2017 -0400 +++ b/GRsetFromGEO/GRsetFromGEO.xml Wed Sep 06 06:02:44 2017 -0400 |
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| @@ -1,25 +1,27 @@ <tool id="getGRset" name="GRsetFromGEO"> - <description>downloads data from GEO</description> - <requirements> -<requirement type="package" version="1.20.0">bioconductor-minfi</requirement> -<requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command>Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output"</command> - <inputs> - <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> - </inputs> - <outputs> - <data format="rdata" name="output" label="output.rdata" /> - </outputs> - <help> + <description>downloads data from GEO</description> + <requirements> + <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> + <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> + </requirements> + <command detect_errors="aggressive"> + Rscript '$__tool_directory__/GRsetFromGEO.R' '$input' '$output' + </command> + <inputs> + <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> + </inputs> + <outputs> + <data format="rdata" name="output" label="output.rdata" /> + </outputs> + <help> **What it does** + This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object + **Input** The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" + **Output** GenomicRatioSet object - </help> + </help> </tool> |