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