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comparison getMETAdata/getMETAdata.xml @ 71:81b5c08c21e1 draft

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author testtool
date Mon, 14 Aug 2017 09:44:57 -0400
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70:759073309c9c 71:81b5c08c21e1
1 <tool id="META" name="getMETAdata" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="1.10.4">r-data.table</requirement>
4 <requirement type="package" version="2.38.4">bioconductor-geoquery</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command> Rscript $__tool_directory__/getMETAdata.R "$GSMTable" "$MetaTable" </command>
10 <inputs>
11 <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable">
12 <validator type="empty_field" message="This field is required."/>
13 </param>
14 </inputs>
15 <outputs>
16 <data format="txt" name="MetaTable" label="MetaData.txt"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="test">
21 <element name="test-data">
22 <collection type="data">
23 <element name="GSMTable" value="test-data/GSMTable.txt" />
24 </collection>
25 </element>
26 </param>
27 <output format="txt" name="MetaTable" label="test-data/MetaTable.txt"/>
28 </test>
29 </tests>
30 <help>
31 **What it does**
32 This R-based tool downloads data from GEO using getGEO from the GEOquery package
33 **Input**
34 A table representing ID of GEO objects for download and parsing
35 **Output**
36 Get a metadata table from NCBI
37 </help>
38 <citations>
39 <citation type="doi">10.1093/bioinformatics/btm254</citation>
40 </citations>
41 </tool>