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comparison GEOQuery.xml @ 0:1024245abc70 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
author sblanck
date Thu, 22 Feb 2018 08:38:22 -0500
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1 <tool id="GEOQuery" name="GEOQuery" version="1.0.0">
2
3 <description>GEOQuery wrapper</description>
4
5 <requirements>
6 <requirement type="package" version="2.42.0">bioconductor-geoquery</requirement>
7 <requirement type="package">r-optparse</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" />
11 <regex match="Warning" source="both" level="warning"/>
12 </stdio>
13
14 <command>
15 <![CDATA[
16 Rscript --vanilla
17 ${__tool_directory__}/GEOQuery.R
18 --id ${GEOQueryID}
19 --transformation ${transformation}
20 --data ${GEOQueryData}
21 --rdata ${GEOQueryRData}
22 --conditions ${conditions}
23 ]]>
24 </command>
25
26 <inputs>
27 <param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
28 <validator type="empty_field"/>
29 </param>
30 <param name="transformation" type="select" label="log2 transformation">
31 <option value="auto">auto</option>
32 <option value="yes">yes</option>
33 <option value="no">no</option>
34 </param>
35 </inputs>
36
37 <outputs>
38 <data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
39 <data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
40 <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>
41 </outputs>
42
43 <tests>
44 <test>
45 <param name="GEOQueryID" value="GSE3524"/>
46 <param name="transformation" value="auto"/>
47 <output name="conditions" file="conditions.cond" ftype="cond"/>
48 </test>
49 </tests>
50
51 <help>
52 <![CDATA[
53 **What it does**
54
55 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.
56 The .cond file is a text file containing one line per sample in the experiment. Each line is made of 3 columns:
57
58 - Sample ID
59 - Condition of the biological sample
60 - Description of the biological sample
61
62 **Example** of .cond file
63 ::
64
65 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
66 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
67 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
68 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
69 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
70
71 **Results**
72
73 - Rdata object containing data for further analysis
74 - Condition (.cond) file summarizing conditions of the experiment
75 - Tabular (.txt) file containing expression data for each sample
76 ]]>
77 </help>
78
79 </tool>