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comparison findSNP/findSNPs.xml @ 0:803decff7ac8 draft

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author testtool
date Sun, 11 Jun 2017 10:00:48 -0400
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1 <tool id="SNPs" name="SNPs" version="1.16.2">
2 <requirements>
3 <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8 <command> Rscript $__tool_directory__/findSNPs.R "$input" "$output" </command>
9 <inputs>
10 <param name="input" format="Rdata"label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
11 </inputs>
12 <outputs>
13 <data format="txt" name="output" label="SNPs.txt"/>
14 </outputs>
15 <tests>
16 <test>
17 <param name="test">
18 <element name="test-data">
19 <collection type="data">
20 <element format="Rdata" name="input" label="test-data/GenomicRatioSet.Rdata"/>
21 </collection>
22 </element>
23 </param>
24 <output format="txt" name="output" label="test-data/findSNP.txt"/>
25 </test>
26 </tests>
27 <help>
28 **What it does**
29 SNPs inside the probe body or at the nucleotide extension can have important consequences on the downstream analysis, these tool offers the possibility to remove such probes
30 **Input**
31 GenomicRatioSet object e.g. output from getGRsetFromGEO tool
32 **Output**
33 Text file with columns containing the SNP information about the probes
34 </help>
35 <citations>
36 <citation type="doi">10.1093/bioinformatics/btu049</citation>
37 </citations>
38 </tool>