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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="LimmaAnalyse" name="Limma analysis" version="1.0.0">
2
3 <description>Performs gene expression analysis thanks to limma</description>
4
5 <requirements>
6 <requirement type="package">bioconductor-biobase</requirement>
7 <requirement type="package">bioconductor-geoquery</requirement>
8 <requirement type="package">bioconductor-geometadb</requirement>
9 <requirement type="package">bioconductor-limma</requirement>
10 <requirement type="package">bioconductor-affy</requirement>
11 <requirement type="package">r-jsonlite</requirement>
12 <requirement type="package">r-dplyr</requirement>
13 <requirement type="package">r-optparse</requirement>
14 </requirements>
15
16 <stdio>
17 <exit_code range="1:" />
18 <regex match="Warning" source="both" level="warning"/>
19 </stdio>
20
21 <command>
22 <![CDATA[
23 Rscript
24 ${__tool_directory__}/Analyse.R
25 --rdatainput ${rdataset}
26 --conditions ${conditions}
27 --selectcondition1 "${selectCondition1}"
28 --selectcondition2 "${selectCondition2}"
29 --nbresult ${nbresult}
30 --rdataoutput ${result_export_eset}
31 --htmloutput $result_html
32 --htmloutputpath $result_html.files_path
33 --tabularoutput $result_tabular
34 --htmltemplate ${__tool_directory__}/Analyse_tpl.html
35 --tooldirectory ${__tool_directory__}
36 ]]>
37 </command>
38
39 <inputs>
40 <param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
41 <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
42 <param name="selectCondition1" type="select" label="condition 1">
43 <options from_dataset="conditions">
44 <column name="name" index="1"/>
45 <column name="value" index="1"/>
46 <filter type="unique_value" column="1"/>
47 </options>
48 </param>
49 <param name="selectCondition2" type="select" label="condition 2">
50 <options from_dataset="conditions">
51 <column name="name" index="1"/>
52 <column name="value" index="1"/>
53 <filter type="unique_value" column="1"/>
54 </options>
55 </param>
56 <param name="nbresult" type="integer" value="1000" min="1" label="number of top genes" help="Number of genes to be displayed in result datatable"/>
57 </inputs>
58
59 <outputs>
60 <data format="html" name="result_html" label="Results of analysis of ${rdataset.name}"/>
61 <data format="rdata" name="result_export_eset" label="Export of expression set of ${rdataset.name}"/>
62 <data format="tabular" name="result_tabular" label="Text Results of analysis of ${rdataset.name}"/>
63 </outputs>
64
65 <tests>
66 <test>
67 <param name="rdataset" value="GSE3524_data.rdata"/>
68 <param name="conditions" value="conditions.cond"/>
69 <param name="selectCondition1" value="series of 16 tumors"/>
70 <param name="selectCondition2" value="series of 4 normals"/>
71 <param name="nbresult" value="10"/>
72 <output name="result_tabular" file="GSE3524_analysis.tabular" ftype="tabular"/>
73 </test>
74 </tests>
75
76 <help>
77 <![CDATA[
78 **What it does**
79
80 The Limma analysis tool performs single analysis either of data previously retrieved from GEO database or normalized affymetrix .CEL files data.
81 Given a .cond file, it runs a standard limma differential expression analysis.
82
83 **Example** of .cond file
84
85 The .cond file should look like this
86 ::
87
88
89 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
90 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
91 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
92 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
93 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
94
95
96 **Results**
97
98 - Boxplots, p-value histograms and a volcano plot
99 - Table summarizing the differentially expressed genes and their annotations. This table is sortable and requestable.
100 - Rdata object to perform further meta-analysis.
101 ]]>
102 </help>
103
104 </tool>