Mercurial > repos > testtool > get_gr_set

comparison GRsetFromGEO/GRsetFromGEO.xml @ 15:6c3be09de899 draft

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author testtool
date Thu, 29 Jun 2017 08:04:13 -0400
parents 6f7428f907da
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14:c3b28b232e64 15:6c3be09de899
1 <?xml version="1.0" encoding="UTF-8"?> 1 <tool id="GetGEO" name="GRsetFromGEO" version="0.1.0">
2 <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> 2 <requirements>
3 <requirements> 3 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> 4 </requirements>
5 </requirements> 5 <stdio>
6 <stdio> 6 <exit_code range="1:" />
7 <exit_code range="1:" /> 7 </stdio>
8 </stdio> 8 <command><![CDATA[
9 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> 9 Rscript $__tool_directory__/GRsetFromGEO.R -a "$input" > "$output"
10 <inputs> 10 ]]></command>
11 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> 11 <inputs>
12 </inputs> 12 <param type="text" name="input" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
13 <outputs> 13 </inputs>
14 <data format="RDdata" name="output" label="GRsetFromGEO.RData"/> 14 <outputs>
15 </outputs> 15 <data name="output" format="RDdata" label="GRsetFromGEO.RData"/>
16 <tests> 16 </outputs>
17 <test> 17 <tests>
18 <param name="test"> 18 <test>
19 <element name="test-data"> 19 <param name="input" value="GSE51547"/>
20 <collection type="data"> 20 <output name="output" file="test-data/out.RData"/>
21 <element name="GSE" value="GSE51547"/>
22 </collection>
23 </element>
24 </param>
25 <output type="data" format="RData" name="output" label="test-data/out.RData"/>
26 </test> 21 </test>
27 </tests> 22 </tests>
28 <help> 23 <help>**What it does**
29 **What it does** 24 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 25 **Input**
31 **Input** 26 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'" 27 **Output**
33 **Output** 28 GenomicRatioSet object</help>
34 GenomicRatioSet object 29 <citations>
35 </help> 30 <citation type="doi">10.1093/bioinformatics/btu049</citation>
36 <citations> 31 </citations>
37 <citation type="doi">10.1093/bioinformatics/btu049</citation>
38 </citations>
39 </tool> 32 </tool>