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2
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1 <tool id="LimmaAnalyse" name="Limma analysis" version="0.3.0">
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2 <description>Perform gene expression analysis thanks to limma</description>
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5
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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2
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6 <requirements>
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7 <!--container type="docker">sblanck/smagexp</container-->
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8 <requirement type="package" version="0.1.0">r-smagexp</requirement>
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9 </requirements>
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5
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10 <command>
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2
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11 <![CDATA[
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12 Rscript
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13 ${__tool_directory__}/Analyse.R
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5
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14 --rdatainput ${rdataset}
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15 --conditions ${conditions}
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16 --selectcondition1 "${selectCondition1}"
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17 --selectcondition2 "${selectCondition2}"
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18 --nbresult ${nbresult}
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19 --rdataoutput ${result_export_eset}
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20 --htmloutput $result_html
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21 --htmloutputpath $result_html.files_path
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22 --tabularoutput $result_tabular
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23 --htmltemplate ${__tool_directory__}/Analyse_tpl.html
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2
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24 ]]>
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25 </command>
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26
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27 <inputs>
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28 <param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
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29 <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
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30 <param name="selectCondition1" type="select" label="condition 1">
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31 <options from_dataset="conditions">
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32 <column name="name" index="1"/>
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33 <column name="value" index="1"/>
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34 <filter type="unique_value" column="1"/>
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35 </options>
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36 </param>
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37 <!--param name="condition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
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38 <options from_dataset="conditions">
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39 <column name="name" index="2"/>
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40 <column name="value" index="0"/>
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41 <filter type="param_value" ref="selectCondition1" column="1"/>
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42 </options>
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43 </param-->
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44 <param name="selectCondition2" type="select" label="condition 2">
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45 <options from_dataset="conditions">
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46 <column name="name" index="1"/>
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47 <column name="value" index="1"/>
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48 <filter type="unique_value" column="1"/>
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49 </options>
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50 </param>
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5
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51 <!--param name="condition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
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2
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52 <options from_dataset="conditions">
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53 <column name="name" index="2"/>
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54 <column name="value" index="0"/>
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55 <filter type="param_value" ref="selectCondition2" column="1"/>
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56 </options>
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5
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57 </param-->
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58 <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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59 </inputs>
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60 <outputs>
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61 <data format="html" name="result_html" label="Results of analysis of ${rdataset.name}"/>
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62 <data format="rdata" name="result_export_eset" label="Export of expression set of ${rdataset.name}"/>
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63 <data format="tabular" name="result_tabular" label="Text Results of analysis of ${rdataset.name}"/>
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64
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65 </outputs>
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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 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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71 Given a .cond file, it runs a standard limma differential expression analysis.
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72
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73 **Example** of .cond file
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74
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75 The .cond file should look like this
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76 ::
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77
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5
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78
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2
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79 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
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80 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
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81 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
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82 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
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83 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
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84
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85
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86 **Results**
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87
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88 - Boxplots, p-value histograms and a volcano plot
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89 - Table summarizing the differentially expressed genes and their annotations. This table is sortable and requestable.
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90 - Rdata object to perform further meta-analysis.
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91 ]]>
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92 </help>
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93
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94 </tool>
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