|
0
|
1 <tool id="metaMAGEOQuery" name="GEOanalyse" version="0.1.0">
|
|
|
2 <description>GEOAnalyse wrapper</description>
|
|
|
3 <requirements>
|
|
|
4 <container type="docker">sblanck/testtool:latest</container>
|
|
|
5 </requirements>
|
|
|
6 <command>
|
|
|
7
|
|
|
8 /galaxy-tools/stderr_wrapper.py Rscript
|
|
|
9 /galaxy-tools/transcriptomics/GEOanalyse/GEOAnalyse.R
|
|
|
10 "${rdataset}"
|
|
|
11 "${selectCondition}"
|
|
|
12 $result_html
|
|
|
13 $result_html.files_path
|
|
|
14 /galaxy-tools/transcriptomics/GEOanalyse/GEOAnalyse_tpl.html
|
|
|
15
|
|
|
16 </command>
|
|
|
17
|
|
|
18 <inputs>
|
|
|
19
|
|
|
20 <param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
|
|
|
21
|
|
|
22 <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
|
|
|
23
|
|
|
24 <param name="selectCondition" type="select" label="case condition">
|
|
|
25 <options from_dataset="conditions">
|
|
|
26 <column name="name" index="0"/>
|
|
|
27 <column name="value" index="0"/>
|
|
|
28 </options>
|
|
|
29 </param>
|
|
|
30
|
|
|
31 </inputs>
|
|
|
32 <outputs>
|
|
|
33 <data format="html" name="result_html" label="Annotations"/>
|
|
|
34
|
|
|
35 </outputs>
|
|
|
36
|
|
|
37 <help>
|
|
|
38 NOTE: This metaMA wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
|
|
|
39 </help>
|
|
|
40
|
|
|
41 </tool>
|
