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annotate MetaRNAseq.xml @ 39:07ac07715f22 draft default tip

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 7026b0fbe3611962c37c7f9b5f001434f059e32c
author sblanck
date Tue, 26 Jun 2018 04:14:25 -0400
parents 25b828010ca9
children
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1 <tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.1.0">
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3 <description>Performs meta-analysis thanks to metaRNAseq</description>
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5 <requirements>
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6 <requirement type="package">bioconductor-affy</requirement>
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7 <requirement type="package">bioconductor-annaffy</requirement>
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8 <requirement type="package">bioconductor-geoquery</requirement>
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9 <requirement type="package">r-venndiagram</requirement>
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10 <requirement type="package">r-jsonlite</requirement>
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11 <requirement type="package">r-metarnaseq</requirement>
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12 <requirement type="package">r-optparse</requirement>
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13 <requirement type="package" version="1.3.3">r-upsetr</requirement>
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14 </requirements>
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16 <stdio>
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17 <exit_code range="1:" />
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18 <regex match="Warning" source="both" level="warning"/>
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19 </stdio>
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21 <command>
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23 <![CDATA[
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24 Rscript
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25 ${__tool_directory__}/MetaRNASeq.R
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26 --input "#for $s in $studies:
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27 ${s.input};
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28 #end for
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29 "
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30 --inputName "#for $s in $studies:
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31 ${s.input.name};
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32 #end for
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33 "
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34 --nbreplicates "#for $s in $studies:
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35 ${s.nbreplicates};
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36 #end for
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37 "
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38
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39 --fdr $fdr
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40 --result $top_table
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41 --htmloutput $result_html
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42 --htmloutputpath $result_html.extra_files_path
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43 --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html
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44 ]]>
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46 </command>
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48 <inputs>
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49 <repeat name="studies" title="Study results" min="2" default="2" help="DESeq2 Result file and number of replicate of the study">
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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"/>
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51 <param name="nbreplicates" type="integer" value="10" label="Number of replicates" help="Number of replicates of the study"/>
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52 </repeat>
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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"/>
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54 </inputs>
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57 <outputs>
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58 <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
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59 <data format="html" name="result_html" label="Charts for ${tool.name} on ${on_string}"/>
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60 </outputs>
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62 <tests>
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64 </tests>
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66 <help>
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67 <![CDATA[
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68 **What it does**
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69
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70 Given several DESeq2 results this tool runs a meta-analysis using the metaRNAseq R package.
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71
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72 **Inputs**
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73 - At least 2 studies, and for each study
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74 - Results of DESeq2 study
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75 - Number of replicates of the study
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76 - A FDR Threshold for a gene to be declared differentially expressed
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77
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78
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79 **Results**
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81 - Venn Diagram or upsetR diagram (when the number of studies is greater than 2) summarizing the results of the meta-analysis
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82 - A list of indicators to evaluate the quality of the performance of the meta-analysis
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83
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84 - DE : Number of differentially expressed genes
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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
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86 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis
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87 - DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
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88 - IRR (Integration-driven Revision) : corresponding proportion of Loss
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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.
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91 ]]>
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92 </help>
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94 </tool>