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comparison GRsetFromGEO/GRsetFromGEO.xml @ 20:40d7bdac6322 draft

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author testtool
date Mon, 03 Jul 2017 07:13:53 -0400
parents 6c3be09de899
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19:0a619d0e45fd 20:40d7bdac6322
1 <tool id="GetGEO" name="GRsetFromGEO" version="0.1.0"> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <requirements> 2 <tool id="GetGEO" name="GRsetFromGEO" version="1.16.2">
3 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> 3 <requirements>
4 </requirements> 4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
5 <stdio> 5 </requirements>
6 <exit_code range="1:" /> 6 <stdio>
7 </stdio> 7 <exit_code range="1:" />
8 <command><![CDATA[ 8 </stdio>
9 Rscript $__tool_directory__/GRsetFromGEO.R -a "$input" > "$output" 9 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output" </command>
10 ]]></command> 10 <inputs>
11 <inputs> 11 <param name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
12 <param type="text" name="input" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> 12 </inputs>
13 </inputs> 13 <outputs>
14 <outputs> 14 <data format="RDdata" name="output" label="GRsetFromGEO.RData"/>
15 <data name="output" format="RDdata" label="GRsetFromGEO.RData"/> 15 </outputs>
16 </outputs> 16 <tests>
17 <tests> 17 <test>
18 <test> 18 <param name="test">
19 <param name="input" value="GSE51547"/> 19 <element name="test-data">
20 <output name="output" file="test-data/out.RData"/> 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"/>
21 </test> 26 </test>
22 </tests> 27 </tests>
23 <help>**What it does** 28 <help>
24 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object 29 **What it does**
25 **Input** 30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
26 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" 31 **Input**
27 **Output** 32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
28 GenomicRatioSet object</help> 33 **Output**
29 <citations> 34 GenomicRatioSet object
30 <citation type="doi">10.1093/bioinformatics/btu049</citation> 35 </help>
31 </citations> 36 <citations>
37 <citation type="doi">10.1093/bioinformatics/btu049</citation>
38 </citations>
32 </tool> 39 </tool>