annotate getGEO/getGEO.xml @ 12:fafbd5bb1f05 draft

Uploaded
author testtool
date Wed, 18 Jan 2017 11:52:53 -0500
parents 2418fe6a0d12
children a0fefac1e0e1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
1 <tool id="GEO" name="getGEO" version="1.16.2">
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
2 <requirements>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
3 <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
4 </requirements>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
5 <stdio>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
6 <exit_code range="1:" />
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
7 </stdio>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
8 <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
9 <inputs>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
10 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
11 <validator type="empty_field" message="This field is required."/>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
12 </param>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
13 </inputs>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
14 <outputs>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
15 <data format="csv" name="MetaTable" label="MetaData.csv"/>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
16 <data format="csv" name="IlmnTable" label="IlmnData.csv"/>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
17 <data format="csv" name="gmTable" label="gmSet.csv"/>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
18 </outputs>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
19 <tests>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
20 <test>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
21 <param name="test">
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
22 <element name="test-data">
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
23 <collection type="data">
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
24 <element name="GSMTable" value="test-data/input.csv" />
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
25 </collection>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
26 </element>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
27 </param>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
28 <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
29 <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
30 <output format="csv" name="gmTable" label="test-data/gmTable.csv"/>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
31 </test>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
32 </tests>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
33 <help>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
34 **Description**
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
35 </help>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
36 <citations>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
37 GEO
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
38 </citations>
2418fe6a0d12 Uploaded
testtool
parents:
diff changeset
39 </tool>