Mercurial > repos > testtool > get_gr_set

comparison GRsetFromGEO/GRsetFromGEO.xml @ 29:5d796e9a96ae draft

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author testtool
date Mon, 10 Jul 2017 09:09:09 -0400
parents ab34c2e8e533
children 4f157ee63207
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28:ab34c2e8e533 29:5d796e9a96ae
1 <tool id="getGRset" name="GRsetFromGEO"> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <description>downloads data from GEO</description> 2 <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> 4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
5 </requirements> 5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
6 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command> 9 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command>
7 <inputs> 10 <inputs>
8 <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> 11 <param name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
9 </inputs> 12 </inputs>
10 <outputs> 13 <outputs>
11 <data format="RDdata" name="output" label="output.RData" /> 14 <data format="RDdata" name="output" label="GRsetFromGEO.RData"/>
12 </outputs> 15 </outputs>
16 <tests>
17 <test>
18 <param name="test">
19 <element name="test-data">
20 <collection type="data">
21 <element name="input" value="GSE51547"/>
22 </collection>
23 </element>
24 </param>
25 <output type="data" format="RData" name="output" label="test-data/out.RData"/>
26 </test>
27 </tests>
13 <help> 28 <help>
14 **What it does** 29 **What it does**
15 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object 30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
16 **Input** 31 **Input**
17 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" 32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
18 **Output** 33 **Output**
19 GenomicRatioSet object 34 GenomicRatioSet object
20 </help> 35 </help>
36 <citations>
37 <citation type="doi">10.1093/bioinformatics/btu049</citation>
38 </citations>
21 </tool> 39 </tool>