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author sblanck
date Tue, 26 Jun 2018 04:14:25 -0400
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1 <tool id="LimmaAnalyse" name="Limma analysis" version="1.0.0">
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3 <description>Performs gene expression analysis thanks to limma</description>
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5 <requirements>
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6 <requirement type="package">bioconductor-biobase</requirement>
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7 <requirement type="package">bioconductor-geoquery</requirement>
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8 <requirement type="package">bioconductor-geometadb</requirement>
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9 <requirement type="package">bioconductor-limma</requirement>
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10 <requirement type="package">bioconductor-affy</requirement>
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11 <requirement type="package">r-jsonlite</requirement>
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12 <requirement type="package">r-dplyr</requirement>
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13 <requirement type="package">r-optparse</requirement>
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14 </requirements>
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15
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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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20
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21 <command>
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22 <![CDATA[
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23 Rscript
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24 ${__tool_directory__}/Analyse.R
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25 --rdatainput ${rdataset}
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26 --conditions ${conditions}
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27 --selectcondition1 "${selectCondition1}"
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28 --selectcondition2 "${selectCondition2}"
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29 --nbresult ${nbresult}
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30 --rdataoutput ${result_export_eset}
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31 --htmloutput $result_html
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32 --htmloutputpath $result_html.files_path
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33 --tabularoutput $result_tabular
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34 --htmltemplate ${__tool_directory__}/Analyse_tpl.html
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35 --tooldirectory ${__tool_directory__}
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36 ]]>
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37 </command>
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38
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39 <inputs>
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40 <param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
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41 <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
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42 <param name="selectCondition1" type="select" label="condition 1">
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43 <options from_dataset="conditions">
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44 <column name="name" index="1"/>
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45 <column name="value" index="1"/>
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46 <filter type="unique_value" column="1"/>
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47 </options>
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48 </param>
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49 <param name="selectCondition2" type="select" label="condition 2">
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50 <options from_dataset="conditions">
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51 <column name="name" index="1"/>
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52 <column name="value" index="1"/>
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53 <filter type="unique_value" column="1"/>
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54 </options>
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55 </param>
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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"/>
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57 </inputs>
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58
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59 <outputs>
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60 <data format="html" name="result_html" label="Results of analysis of ${rdataset.name}"/>
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61 <data format="rdata" name="result_export_eset" label="Export of expression set of ${rdataset.name}"/>
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62 <data format="tabular" name="result_tabular" label="Text Results of analysis of ${rdataset.name}"/>
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="rdataset" value="GSE3524_data.rdata"/>
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68 <param name="conditions" value="conditions.cond"/>
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69 <param name="selectCondition1" value="series of 16 tumors"/>
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70 <param name="selectCondition2" value="series of 4 normals"/>
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71 <param name="nbresult" value="10"/>
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72 <output name="result_tabular" file="GSE3524_analysis.tabular" ftype="tabular"/>
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73 </test>
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74 </tests>
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75
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76 <help>
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77 <![CDATA[
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78 **What it does**
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79
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80 The Limma analysis tool performs single analysis either of data previously retrieved from GEO database or normalized affymetrix .CEL files data.
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81 Given a .cond file, it runs a standard limma differential expression analysis.
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82
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83 **Example** of .cond file
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84
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85 The .cond file should look like this
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86 ::
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87
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88
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89 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
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90 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
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91 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
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92 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
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93 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
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95
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96 **Results**
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97
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98 - Boxplots, p-value histograms and a volcano plot
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99 - Table summarizing the differentially expressed genes and their annotations. This table is sortable and requestable.
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100 - Rdata object to perform further meta-analysis.
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101 ]]>
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102 </help>
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103
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104 </tool>