|
2
|
1 <tool id="GEOQuery" name="GEOQuery">
|
|
|
2 <description>GEOQuery wrapper</description>
|
|
|
3 <requirements>
|
|
|
4 <!--container type="docker">sblanck/smagexp</container-->
|
|
|
5 <requirement type="package" version="0.1.0">r-smagexp</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command interpreter="python">
|
|
|
8 <![CDATA[
|
|
|
9 stderr_wrapper.py Rscript
|
|
|
10 ${__tool_directory__}/GEOQuery.R
|
|
|
11 $GEOQueryID
|
|
|
12 $GEOQueryData
|
|
|
13 $GEOQueryRData
|
|
|
14 $conditions
|
|
|
15 $transformation
|
|
|
16 ]]>
|
|
|
17 </command>
|
|
|
18
|
|
|
19 <inputs>
|
|
|
20 <param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
|
|
|
21 <validator type="empty_field"/>
|
|
|
22 </param>
|
|
|
23 <param name="transformation" type="select" label="log2 transformation">
|
|
|
24 <option value="auto">auto</option>
|
|
|
25 <option value="yes">yes</option>
|
|
|
26 <option value="no">no</option>
|
|
|
27 </param>
|
|
|
28 </inputs>
|
|
|
29
|
|
|
30 <outputs>
|
|
|
31 <data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
|
|
|
32 <data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
|
|
|
33 <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>
|
|
|
34 </outputs>
|
|
|
35 <help>
|
|
|
36 <![CDATA[
|
|
|
37 **What it does**
|
|
|
38
|
|
|
39 This tool fetches microarray data directly from GEO database, based on the GEOQuery R package. Given a GSE accession ID, it returns an Rdata object containing the data and a text file (.cond file) summarizing the conditions of the experiment.
|
|
|
40 The .cond file is a text file containing one line per sample in the experiment. Each line is made of 3 columns:
|
|
|
41
|
|
|
42 - Sample ID
|
|
|
43 - Condition of the biological sample
|
|
|
44 - Description of the biological sample
|
|
|
45
|
|
|
46 **Example** of .cond file
|
|
|
47 ::
|
|
|
48
|
|
|
49 Sample ID Condition Description
|
|
|
50 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
|
|
|
51 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
|
|
|
52 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
|
|
|
53 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
|
|
|
54 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
|
|
|
55
|
|
|
56 **Results**
|
|
|
57
|
|
|
58 - Rdata object containing data for further analysis
|
|
|
59 - Condition (.cond) file summarizing conditions of the experiment
|
|
|
60 - Tabular (.txt) file containing expression data for each sample
|
|
|
61 ]]>
|
|
|
62
|
|
|
63 </help>
|
|
|
64
|
|
|
65
|
|
|
66 </tool>
|
