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comparison MetaRNAseq.xml @ 6:3ce32282f6a4 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 228bd64b01f184d5d8ebc9f65fe0add2d45ed4fe
author sblanck
date Tue, 26 Jun 2018 08:54:45 -0400
parents 63355796cdc8
children aedbf50acb4a
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5:ca46ad51fe5a 6:3ce32282f6a4
1 <tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.0.0"> 1 <tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.1.0">
2 2
3 <description>Performs meta-analysis thanks to metaRNAseq</description> 3 <description>Performs meta-analysis thanks to metaRNAseq</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package">bioconductor-affy</requirement> 6 <requirement type="package">bioconductor-affy</requirement>
8 <requirement type="package">bioconductor-geoquery</requirement> 8 <requirement type="package">bioconductor-geoquery</requirement>
9 <requirement type="package">r-venndiagram</requirement> 9 <requirement type="package">r-venndiagram</requirement>
10 <requirement type="package">r-jsonlite</requirement> 10 <requirement type="package">r-jsonlite</requirement>
11 <requirement type="package">r-metarnaseq</requirement> 11 <requirement type="package">r-metarnaseq</requirement>
12 <requirement type="package">r-optparse</requirement> 12 <requirement type="package">r-optparse</requirement>
13 <requirement type="package" version="1.3.3">r-upsetr</requirement>
13 </requirements> 14 </requirements>
14 15
15 <stdio> 16 <stdio>
16 <exit_code range="1:" /> 17 <exit_code range="1:" />
17 <regex match="Warning" source="both" level="warning"/> 18 <regex match="Warning" source="both" level="warning"/>
18 </stdio> 19 </stdio>
19 20
20 <command> 21 <command>
21 22
22 <![CDATA[ 23 <![CDATA[
23 Rscript 24 Rscript
24 ${__tool_directory__}/MetaRNASeq.R 25 ${__tool_directory__}/MetaRNASeq.R
25 --input "#for $input in $inputs# $input;$input.name, #end for#" 26 --input "#for $s in $studies:
27 ${s.input};
28 #end for
29 "
30 --inputName "#for $s in $studies:
31 ${s.input.name};
32 #end for
33 "
34 --nbreplicates "#for $s in $studies:
35 ${s.nbreplicates};
36 #end for
37 "
38
39 --fdr $fdr
26 --result $top_table 40 --result $top_table
27 --htmloutput $result_html 41 --htmloutput $result_html
28 --htmloutputpath $result_html.extra_files_path 42 --htmloutputpath $result_html.extra_files_path
29 --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html 43 --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html
30 ]]> 44 ]]>
45
31 </command> 46 </command>
32 47
33 <inputs> 48 <inputs>
34 <param format="tabular" name="inputs" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/> 49 <repeat name="studies" title="Study results" min="2" default="2" help="DESeq2 Result file and number of replicate of the study">
50 <param format="tabular" name="input" multiple="false" type="data" optional="false" label="DESeq2 result file" help="Must have the same number of row in each study"/>
51 <param name="nbreplicates" type="integer" value="10" label="Number of replicates" help="Number of replicates of the study"/>
52 </repeat>
53 <param name="fdr" type="float" value="0.05" label="FDR" min="0" max="1" help="Adjusted p-value threshold to be declared differentially expressed"/>
35 </inputs> 54 </inputs>
55
36 56
37 <outputs> 57 <outputs>
38 <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/> 58 <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
39 <data format="html" name="result_html" label="Charts for ${tool.name} on ${on_string}"/> 59 <data format="html" name="result_html" label="Charts for ${tool.name} on ${on_string}"/>
40 </outputs> 60 </outputs>
42 <tests> 62 <tests>
43 63
44 </tests> 64 </tests>
45 65
46 <help> 66 <help>
67 <![CDATA[
68 **What it does**
69
70 Given several DESeq2 results this tool runs a meta-analysis using the metaRNAseq R package.
71
72 **Inputs**
73 - At least 2 studies, and for each study
74 - Results of DESeq2 study
75 - Number of replicates of the study
76 - A FDR Threshold for a gene to be declared differentially expressed
77
47 78
79 **Results**
80
81 - Venn Diagram or upsetR diagram (when the number of studies is greater than 2) summarizing the results of the meta-analysis
82 - A list of indicators to evaluate the quality of the performance of the meta-analysis
83
84 - DE : Number of differentially expressed genes
85 - IDD (Integration Driven discoveries) : number of genes that are declared differentially expressed in the meta-analysis that were not identified in any of the single studies alone
86 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis
87 - DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
88 - IRR (Integration-driven Revision) : corresponding proportion of Loss
89
90 It also generates a text file containing summarization of the results of each single analysis and meta-analysis. Potential conflicts between single analyses are indicated by zero values in the "signFC" column.
91 ]]>
48 </help> 92 </help>
49 93
50 </tool> 94 </tool>