Mercurial > repos > proteore > proteore_topgo

annotate topGO.xml @ 14:4ebc0fa10ebd draft

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author proteore
date Fri, 26 Oct 2018 08:26:00 -0400
parents bb92de0eb880
children da0bf437245d
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1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.10.26">
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2 <description>(Human, Mouse, Rat) (topGO)</description>
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3 <requirements>
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4 <requirement type="package" version="3.4.1">R</requirement>
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5 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
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6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
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7 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
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8 <requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement>
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9 <requirement type="package" version="3.5.0">bioconductor-org.ce.eg.db</requirement>
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10 <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement>
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11 <requirement type="package" version="3.5.0">bioconductor-org.sc.sgd.db</requirement>
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12 <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement-->
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13 <requirement type="package" version="1.56.0">bioconductor-graph</requirement>
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14 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
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15 <requirement type="package" version="3.5.0">bioconductor-go.db</requirement>
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16 <requirement type="package" version="2.30.0">bioconductor-topgo</requirement>
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17 </requirements>
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18 <stdio>
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19 <exit_code range="1:" />
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20 </stdio>
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21 <command><![CDATA[
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23 Rscript --vanilla $__tool_directory__/topGO_enrichment.R
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24 --inputtype="$inputtype.filetype"
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25 --input='$inputtype.genelist'
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27 #if $inputtype.filetype == "file"
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28 --column='$inputtype.column'
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29 --header='$inputtype.header'
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30 #end if
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31
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32 --ontology='$ontocat'
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33 --option='$option'
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34 --threshold='$threshold'
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35 --correction='$correction'
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36 --textoutput='$textoutput'
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37 --barplotoutput='$barplot'
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38 --dotplotoutput='$dotplot'
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39 --geneuniverse='$geneuniverse'
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40 --background="$background_genes.background"
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41
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42 #if $background_genes.background == "true"
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43 --background_genes="$background_genes.inputtype.genelist"
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44 --background_input_type="$background_genes.inputtype.filetype"
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45 #if $background_genes.inputtype.filetype == "file"
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46 --background_header="$background_genes.inputtype.header"
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47 --background_column="$background_genes.inputtype.column"
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48 #end if
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49 #end if
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50
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51 ]]></command>
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52
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53 <inputs>
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54 <conditional name="inputtype">
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55 <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Converter tool.">
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56 <option value="file" selected="true">Input file containing your identifiers</option>
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57 <option value="copy_paste">Copy/paste your list of IDs</option>
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58 </param>
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59 <when value="copy_paste">
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60 <param name="genelist" type="text" label="Enter a list of identifiers">
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61 <sanitizer>
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62 <valid initial="string.printable">
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63 <remove value="&apos;"/>
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64 </valid>
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65 <mapping initial="none">
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66 <add source="&apos;" target="__sq__"/>
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67 </mapping>
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68 </sanitizer>
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69 </param>
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70 </when>
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71 <when value="file">
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72 <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
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73 <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter 'c1' for column n°1..)" value="c1"/>
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74 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" />
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75 </when>
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76 </conditional>
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77 <conditional name="background_genes">
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78 <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs"/>
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79 <when value="true">
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80 <conditional name="inputtype">
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81 <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Mapping tool.">
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82 <option value="file" selected="true">Input file containing your identifiers</option>
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83 <option value="copy_paste">Copy/paste your list of IDs</option>
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84 </param>
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85 <when value="copy_paste">
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86 <param name="genelist" type="text" label="Enter a list of identifiers">
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87 <sanitizer>
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88 <valid initial="string.printable">
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89 <remove value="&apos;"/>
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90 </valid>
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91 <mapping initial="none">
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92 <add source="&apos;" target="__sq__"/>
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93 </mapping>
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94 </sanitizer>
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95 </param>
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96 </when>
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97 <when value="file">
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98 <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
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99 <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter 'c1' for column n°1..)" value="c1"/>
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100 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" />
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101 </when>
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102 </conditional>
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103 </when>
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104 <when value="false"/>
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105 </conditional>
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106 <param name="geneuniverse" type="select" label="Select a specie">
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107 <!--option value="org.At.tair.db" >Arabidopsis</option-->
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108 <option value="org.Ce.eg.db" >Worm (C. elegans)</option>
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109 <option value="org.Dm.eg.db" >Fly (D. melanogaster)</option>
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110 <option value="org.Hs.eg.db" selected="true">Human (H. sapiens)</option>
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111 <option value="org.Mm.eg.db" >Mouse (M. musculus)</option>
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112 <option value="org.Rn.eg.db" >Rat (Rattus norvegicus)</option>
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113 <option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option>
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114 </param>
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115 <param name="ontocat" type="select" label="Ontology category">
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116 <option value="BP" >Biological Process</option>
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117 <option value="CC" >Cellular Component</option>
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118 <option value="MF" >Molecular Function</option>
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119 </param>
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120 <param name="option" type="select" label="Choose the topGO option for your analysis">
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121 <option value="classic" >Classic fisher test</option>
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122 <option value="elim" selected="true">Elim</option>
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123 <option value="weight01" >Weight01</option>
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124 <option value="parentchild" >ParentChild</option>
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125 </param>
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126 <param name="threshold" type="text" label="Enter the p-value threshold level under the form 1e-level wanted (e.g : 1e-3)" value="1e-3"/>
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127 <param name="correction" label="Choose a correction for multiple testing" type="select">
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128 <option value="none" >None</option>
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129 <option value="holm">Holm correction</option>
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130 <option value="hochberg" >Hochberg correction</option>
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131 <option value="hommel" >Hommel correction</option>
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132 <option value="bonferroni" >Bonferroni correction</option>
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133 <option value="BH" selected="true">Benjamini and Hochberg</option>
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134 <option value="BY" >Benjamini and Yekutieli</option>
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135 <option value="fdr" >FDR</option>
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136 </param>
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137 <param name="textoutput" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a text file for results" />
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138 <param name="barplot" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a barplot of over-represented GO terms" />
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139 <param name="dotplot" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a dotplot of over-represented GO terms" />
0
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140 </inputs>
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141 <outputs>
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142
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143 <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result">
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144 <filter>textoutput</filter>
0
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145 </data>
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146
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147 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
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148 <filter>barplot</filter>
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149 </data>
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150
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151 <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
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152 <filter>dotplot</filter>
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153 </data>
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154
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155 </outputs>
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156 <tests>
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157 <test>
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158 <conditional name="inputtype">
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159 <param name="filetype " value="tabfile"/>
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160 <param name="genelist" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/>
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161 <param name="column" value="c8"/>
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162 <param name="header" value="TRUE"/>
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163 </conditional>
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164 <param name="ontocat" value="BP"/>
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165 <param name="option" value="elim"/>
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166 <param name="threshold" value="1e-3"/>
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167 <param name="correction" value="BH"/>
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168 <conditional name="condtext">
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169 <param name="textoutput" value="TRUE"/>
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170 </conditional>
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171 <conditional name="condbar">
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172 <param name="barplotoutput" value="TRUE"/>
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173 </conditional>
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174 <conditional name="conddot">
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175 <param name="dotoutput" value="TRUE"/>
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176 </conditional>
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177 <param name="geneuniverse" value="org.Hs.eg.db"/>
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178 <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/>
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179 <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/>
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180 <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/>
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181 </test>
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182 </tests>
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183 <help><![CDATA[
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184
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185
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186 **Galaxy component based on R package topGO.**
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187
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188 **Input required**
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189
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190 This component works with Ensembl gene ids (e.g : ENSG0000013618). You can
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191 copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab)
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192 where there are contained.
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193
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194 **Principle**
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195
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196 This component provides the GO terms representativity of a gene list in one ontology category (Biological Process "BP", Cellular Component "CC", Molecular Function "MF"). This representativity is evaluated in comparison to the background list of all human genes associated associated with GO terms of the chosen category (BP,CC,MF). This background is given by the R package "org.Hs.eg.db", which is a genome wide association package for **human**.
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197
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198 **Output**
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199
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200 Three kind of outputs are available : a textual output, a barplot output and
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201 a dotplot output.
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202
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203 *Textual output* :
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204 The text output lists all the GO-terms that were found significant under the specified threshold.
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205
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206
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207 The different fields are as follow :
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208
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209 - Annotated : number of genes in org.Hs.eg.db which are annotated with the GO-term.
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210
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211 - Significant : number of genes belonging to your input which are annotated with the GO-term.
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212
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213 - Expected : show an estimate of the number of genes a node of size Annotated would have if the significant genes were to be randomly selected from the gene universe.
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214
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215 - pvalues : pvalue obtained after the test
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216
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217 - ( qvalues : additional column with adjusted pvalues )
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218
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219
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220 **Tests**
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221
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222 topGO provides a classic fisher test for evaluating if some GO terms are over-represented in your gene list, but other options are also provided (elim, weight01,parentchild). For the merits of each option and their algorithmic descriptions, please refer to topGO manual :
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223 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
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224
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225 **Multiple testing corrections**
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226
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227 Furthermore, the following corrections for multiple testing can also be applied :
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228
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229 - holm
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230
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231 - hochberg
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232
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233 - hommel
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234
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235 - bonferroni
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236
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237 - BH
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238
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239 - BY
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240
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241 - fdr
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242
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243 -----
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244
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245 .. class:: infomark
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246
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247 **Authors**
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248
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249 Alexa A and Rahnenfuhrer J (2016). topGO: Enrichment Analysis for Gene Ontology. R package version 2.30.0.
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250
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251 **Galaxy integration**
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252
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253 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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254
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255 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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256
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257 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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258
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259 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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260
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261 ]]></help>
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262 <citations>
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263 </citations>
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264
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265 </tool>