Mercurial > repos > proteore > proteore_topgo

annotate topGO.xml @ 18:36c97ab06d40 draft

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author proteore
date Mon, 17 Dec 2018 11:05:04 -0500
parents e4f86955692b
children 0014bd289aff
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1 <tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.12.17">
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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="3.6.0">bioconductor-org.ce.eg.db</requirement-->
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10 <!--requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement-->
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11 <!--requirement type="package" version="3.6.0">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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26
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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='$correction'
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36 --textoutput='true'
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37 --plot='$plot'
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38 --geneuniverse='$geneuniverse'
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39 --background="$background_genes.background"
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40
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41 #if $background_genes.background == "true"
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42 --background_genes="$background_genes.inputtype.genelist"
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43 --background_input_type="$background_genes.inputtype.filetype"
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44 #if $background_genes.inputtype.filetype == "file"
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45 --background_header="$background_genes.inputtype.header"
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46 --background_column="$background_genes.inputtype.column"
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47 #end if
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48 #end if
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49
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50 ]]></command>
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51
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52 <inputs>
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53 <conditional name="inputtype">
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54 <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene only)" help="Copy/paste or from a file">
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55 <option value="file" selected="true">Input file containing your IDs</option>
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56 <option value="copy_paste">Copy/paste your list of IDs</option>
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57 </param>
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58 <when value="copy_paste">
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59 <param name="genelist" type="text" label="Enter a list of IDs">
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60 <sanitizer>
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61 <valid initial="string.printable">
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62 <remove value="&apos;"/>
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63 </valid>
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64 <mapping initial="none">
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65 <add source="&apos;" target="__sq__"/>
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66 </mapping>
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67 </sanitizer>
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68 </param>
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69 </when>
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70 <when value="file">
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71 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
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72 <param name="column" type="text" label="Column number of IDs" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on"/>
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73 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
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74 </when>
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75 </conditional>
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76 <conditional name="background_genes">
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77 <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs ?"/>
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78 <when value="true">
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79 <conditional name="inputtype">
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80 <param name="filetype" type="select" label="Enter your background IDs (Ensembl gene IDs)" help="(e.g : ENSG00000139618)">
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81 <option value="file" selected="true">Input file containing your background IDs</option>
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82 <option value="copy_paste">Copy/paste your background IDs</option>
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83 </param>
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84 <when value="copy_paste">
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85 <param name="genelist" type="text" label="Copy/paste your background IDs" help="IDs must be separated by spaces into the form field, for example: ENSG00000139618 ENSG00000007350">
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86 <sanitizer>
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87 <valid initial="string.printable">
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88 <remove value="&apos;"/>
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89 </valid>
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90 <mapping initial="none">
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91 <add source="&apos;" target="__sq__"/>
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92 </mapping>
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93 </sanitizer>
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94 </param>
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95 </when>
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96 <when value="file">
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97 <param name="genelist" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help=""/>
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98 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header ?" />
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99 <param name="column" type="text" label="Column number of IDs" value="c1" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on"/>
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100 </when>
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101 </conditional>
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102 </when>
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103 <when value="false"/>
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104 </conditional>
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105 <param name="geneuniverse" type="select" label="Species">
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106 <!--option value="org.At.tair.db" >Arabidopsis</option-->
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107 <!--option value="org.Ce.eg.db" >Worm (C. elegans)</option-->
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108 <!--option value="org.Dm.eg.db" >Fly (D. melanogaster)</option-->
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109 <option value="org.Hs.eg.db" selected="true">Human (Homo sapiens)</option>
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110 <option value="org.Mm.eg.db" >Mouse (Mouse musculus)</option>
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111 <option value="org.Rn.eg.db" >Rat (Rattus norvegicus)</option>
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112 <!--option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option-->
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113 </param>
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114 <param name="ontocat" type="select" label="GO terms category">
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115 <option value="BP" >Biological Process</option>
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116 <option value="CC" >Cellular Component</option>
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117 <option value="MF" >Molecular Function</option>
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118 </param>
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119 <param name="option" type="select" label="Select the topGO parameter (see user doc)">
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120 <option value="classic" >Classic fisher test</option>
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121 <option value="elim" selected="true">Elim</option>
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122 <option value="weight01" >Weight01</option>
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123 <option value="parentchild" >ParentChild</option>
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124 </param>
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125 <param name="threshold" type="text" label="p-value threshold (e.g : 1e-3)" value="1e-3"/>
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126 <param name="correction" label="Multiple testing procedure (p-value adjustment)" type="select">
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127 <option value="none" >None</option>
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128 <option value="holm">Holm correction</option>
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129 <option value="hochberg" >Hochberg correction</option>
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130 <option value="hommel" >Hommel correction</option>
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131 <option value="bonferroni" >Bonferroni correction</option>
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132 <option value="BH" selected="true">Benjamini and Hochberg</option>
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133 <option value="BY" >Benjamini and Yekutieli</option>
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134 <option value="fdr" >FDR</option>
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135 </param>
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136 <!--param name="textoutput" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a text file for results" /-->
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137 <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
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138 <option selected = "true" value="dotplot">dot-plot</option>
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139 <option value="barplot">bar-plot</option>
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140 </param>
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141 </inputs>
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142 <outputs>
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143
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144 <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result">
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145 <filter>textoutput</filter>
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146 </data>
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147
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148 <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
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149 <filter>barplot</filter>
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150 </data>
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151
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152 <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
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153 <filter>dotplot</filter>
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154 </data>
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155
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156 </outputs>
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157 <tests>
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158 <test>
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159 <conditional name="inputtype">
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160 <param name="filetype " value="tabfile"/>
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161 <param name="genelist" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/>
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162 <param name="column" value="c8"/>
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163 <param name="header" value="TRUE"/>
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164 </conditional>
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165 <param name="ontocat" value="BP"/>
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166 <param name="option" value="elim"/>
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167 <param name="threshold" value="1e-3"/>
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168 <param name="correction" value="BH"/>
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169 <conditional name="condtext">
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170 <param name="textoutput" value="TRUE"/>
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171 </conditional>
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172 <conditional name="condbar">
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173 <param name="barplotoutput" value="TRUE"/>
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174 </conditional>
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175 <conditional name="conddot">
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176 <param name="dotoutput" value="TRUE"/>
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177 </conditional>
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178 <param name="geneuniverse" value="org.Hs.eg.db"/>
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179 <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/>
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180 <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/>
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181 <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/>
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182 </test>
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183 </tests>
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184 <help><![CDATA[
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185
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186
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187 **Description**
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188 This tool is based on R package topGO. topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be applied.
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189 **Input required**
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190
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191 This component works with Ensembl gene ids (e.g : ENSG0000013618). You can
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192 copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab)
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193 where there are contained.
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194
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195 **Principle**
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196
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197 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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198
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199 **Output**
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200
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201 Three kind of outputs are available : a textual output, a barplot output and
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202 a dotplot output.
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203
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204 *Textual output* :
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205 The text output lists all the GO-terms that were found significant under the specified threshold.
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206
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207
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208 The different fields are as follow :
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209
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210 - Annotated : number of genes in org.Hs.eg.db which are annotated with the GO-term.
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211
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212 - Significant : number of genes belonging to your input which are annotated with the GO-term.
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213
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214 - 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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215
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216 - pvalues : pvalue obtained after the test
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217
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218 - ( qvalues : additional column with adjusted pvalues )
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219
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220
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221 **Tests**
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222
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223 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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224 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
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225
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226 **Multiple testing corrections**
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227
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228 Furthermore, the following corrections for multiple testing can also be applied :
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229
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230 - holm
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231
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232 - hochberg
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233
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234 - hommel
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235
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236 - bonferroni
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237
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238 - BH
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239
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240 - BY
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241
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242 - fdr
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243
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244 -----
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245
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246 .. class:: infomark
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247
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248 **Authors**
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249
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250 Alexa A and Rahnenfuhrer J (2016). topGO: Enrichment Analysis for Gene Ontology. R package version 2.30.0.
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251
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252 **Galaxy integration**
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253
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254 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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255
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256 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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257
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258 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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259
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260 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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261
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262 ]]></help>
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263 <citations>
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264 </citations>
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265
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266 </tool>