|
31
|
1 <tool id="GEO" name="getGEO" version="1.16.2">
|
|
|
2 <?xml version='1.0' encoding='utf-8'?>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="3.2.1">R</requirement>
|
|
|
5 </requirements>
|
|
32
|
6 <stdio>
|
|
|
7 <exit_code range="1:" level="fatal" />
|
|
|
8 </stdio>
|
|
31
|
9 <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
|
|
|
10 <inputs>
|
|
|
11 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
|
|
|
12 <validator type="empty_field" message="This field is required."/>
|
|
|
13 </param>
|
|
|
14 </inputs>
|
|
|
15 <outputs>
|
|
|
16 <data format="csv" name="MetaTable" label="MetaData.csv"/>
|
|
|
17 <data format="csv" name="IlmnTable" label="IlmnData.csv"/>
|
|
|
18 <data format="csv" name="gmTable" label="gmSet.csv"/>
|
|
|
19 </outputs>
|
|
|
20 <tests>
|
|
|
21 <test>
|
|
|
22 <param name="test">
|
|
|
23 <element name="test-data">
|
|
|
24 <collection type="data">
|
|
|
25 <element name="GSMTable" value="test-data/input.csv" />
|
|
|
26 </collection>
|
|
|
27 </element>
|
|
|
28 </param>
|
|
|
29 <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/>
|
|
|
30 <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/>
|
|
|
31 <output format="csv" name="gmTable" label="test-data/gmTable.csv"/>
|
|
|
32 </test>
|
|
|
33 </tests>
|
|
|
34 <help>
|
|
|
35 **Description**
|
|
|
36 </help>
|
|
|
37 <citations>
|
|
|
38 GEO
|
|
|
39 </citations>
|
|
|
40 </tool>
|
