Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.xml @ 15:601027649251 draft default tip

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"planemo upload commit 6bc2c32177acd823d5025bc90a562e6e6b2a233a"
author proteore
date Tue, 06 Apr 2021 16:59:30 +0000
parents 45b4ede6940e
children
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1 <tool id="goProfiles" name="Compute functional profiles" version="2021.04.03">
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2 <description>(Human, Mouse) [goProfiles]</description>
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3 <requirements>
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4 <requirement type="package" version="4.0.3">r-base</requirement>
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5 <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement>
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6 <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement>
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7 <requirement type="package" version="1.52.0">bioconductor-annotationdbi</requirement>
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8 <requirement type="package" version="2.50.0">bioconductor-biobase</requirement>
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9 <requirement type="package" version="3.12.1">bioconductor-go.db</requirement>
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10 <requirement type="package" version="1.52.0">bioconductor-goprofiles</requirement>
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11 </requirements>
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12 <stdio>
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13 <exit_code range="1:" />
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14 </stdio>
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15 <command><![CDATA[
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16 Rscript $__tool_directory__/goprofiles.R
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17 #if $input.ids == "text"
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18 --input_type="text"
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19 --input="$input.text"
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20 #else
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21 --input_type="file"
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22 --input="$input.file"
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23 --ncol="$input.ncol"
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24 --header="$input.header"
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25 #end if
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26
1
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27 --id_type="$input.id_type"
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28 --onto_opt="$onto_opt"
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29 --plot_opt="$plot_opt"
1
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30 --level="$level"
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31 --per="$per"
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32 --title="$title"
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33 --duplicate="$duplicate"
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34 --text_output="$text_output"
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35 --species="$species" > $log
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36
0
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37 ]]></command>
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38 <inputs>
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39 <conditional name="input" >
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40 <param name="ids" type="select" label="Enter your IDs (Entrez Gene ID or UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
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41 <option value="text">Copy/paste your IDs</option>
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42 <option value="file" selected="true">Input file containing your IDs</option>
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43 </param>
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44 <when value="text" >
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45 <param name="text" type="text" label="Copy/paste your IDs" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
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46 <sanitizer>
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47 <valid initial="string.printable">
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48 <remove value="&apos;"/>
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49 </valid>
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50 <mapping initial="none">
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51 <add source="&apos;" target="__sq__"/>
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52 </mapping>
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53 </sanitizer>
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54 </param>
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55 <param name="id_type" type="select" label="Select type of IDs list" >
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56 <option value="Entrez">Entrez Gene ID</option>
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57 <option value="UniProt">UniProt Accession number</option>
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58 </param>
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59 </when>
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60 <when value="file" >
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61 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
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62 <param name="ncol" type="text" value="c1" 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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63 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
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64 </param>
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65 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
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66 <param name="id_type" type="select" label="Select type of IDs list" >
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67 <option value="Entrez">Entrez Gene ID</option>
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68 <option value="UniProt">Uniprot Accession number</option>
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69 </param>
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70 </when>
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71 </conditional>
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72 <param name="duplicate" type="boolean" checked="true" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
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73 <param name="species" type="select" label="Species">
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74 <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
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75 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
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76 <!--option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option-->
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77 </param>
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78 <param type="select" name="onto_opt" label="Select GO terms category" multiple="True" display="checkboxes" optional="false" >
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79 <option value="CC">Cellular Component (CC)</option>
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80 <option value="MF">Molecular Function (MF)</option>
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81 <option value="BP">Biological Process (BP)</option>
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82 </param>
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83 <param type="select" name="level" label="Ontology level (the higher this number, the deeper the GO level)" >
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84 <option value="1">1</option>
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85 <option value="2" selected="True">2</option>
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86 <option value="3">3</option>
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87 <option value="4">4</option>
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88 <option value="5">5</option>
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89 <option value="6">6</option>
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90 </param>
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91 <param type="boolean" name="per" label="Plot absolute frequencies?" truevalue="TRUE" falsevalue="FALSE" />
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92 <param type="text" name="title" label="Enter title of your figure">
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93 <sanitizer invalid_char=''>
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94 <valid initial="string.printable">
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95 <remove value="&apos;"/>
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96 <remove value="/"/>
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97 </valid>
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98 <mapping>
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99 <add source="&#x20;" target=""/>
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100 </mapping>
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101 </sanitizer>
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102 </param>
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103 <param type="select" name="plot_opt" label="Plot file format">
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104 <option value="PNG" selected="True">png</option>
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105 <option value="JPEG">jpeg</option>
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106 <option value="PDF">pdf</option>
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107 </param>
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108
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109 </inputs>
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110 <outputs>
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111 <data name="log" format="tsv" label="goProfiles log" />
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112 <collection type="list" label="goProfiles text files" name="text_output">
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113 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tsv"/>
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114 </collection>
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115 <collection type="list" label="goProfiles diagram output" name="output" >
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116 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
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117 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" />
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118 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" />
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119 </collection>
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120 </outputs>
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121 <tests>
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122 <test>
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123 <conditional name="input">
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124 <param name="ids" value="file" />
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125 <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
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126 <param name="ncol" value="c1" />
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127 <param name="header" value="true" />
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128 <param name="id_type" value="UniProt" />
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129 </conditional>
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130 <param name="duplicate" value="false"/>
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131 <param name="onto_opt" value="CC,MF,BP" />
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132 <param name="level" value="2" />
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133 <param name="per" value="true" />
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134 <param name="title" value="Test" />
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135 <param name="plot_opt" value="PDF" />
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136 <output_collection name="output" type="list" >
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137 <element name="profile_BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/>
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138 <element name="profile_CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/>
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139 <element name="profile_MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/>
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140 </output_collection>
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141 <output name="log" file="GO_Profile_text_output.tsv"/>
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142 </test>
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143 </tests>
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144 <help><![CDATA[
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145
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146 **Description**
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147
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148 This tool relies on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the
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149 number of identifiers having a hit in each category of this level.
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150
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151 -----
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152
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153 **Input**
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154
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155 Two modes are allowed: either by copy/pasting your IDs (separated by a space) or by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers).
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156 Only entrez gene ID (e.g. 4151) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE.
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157
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158 .. class:: warningmark
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159
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160 In copy/paste mode, the number of IDs considered in input is limited to 5000.
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161
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162 -----
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163
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164 **Parameters**
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165
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166 "Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon)
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167
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168 "Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF)
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169
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170 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 6). In general the higher the level, the more semantically specific the term is.
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171
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172 -----
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173
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174 **Ouput**
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175
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176 Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category.
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177
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178 Text output: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)
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179
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180 -----
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181
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182 .. class:: infomark
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183
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184 Packages used:
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185 - bioconductor-org.hs.eg.db v3.12.0
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186 - bioconductor-org.mm.eg.db v3.12.0
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187 - bioconductor-annotationdbi v1.52.0
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188 - bioconductor-biobase v2.50.0
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189 - bioconductor-go.db v3.12.1
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190 - goprofiles v1.52.0
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191
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192 -----
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193
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194 .. class:: infomark
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195
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196 **Authors**
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197
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198 Salicrú M, Ocaña J, Sánchez-Pla A. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011. 12:401. doi:10.1186/1471-2105-12-401. PubMed PMID: 21999355
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199
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200 -----
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201
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202 .. class:: infomark
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203
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204 **Galaxy integration**
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205
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206 D. Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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207
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208 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform, FR
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209
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210 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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211
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212 Help: contact@proteore.org for any questions or concerns about this tool.
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213 ]]></help>
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214 <citations>
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215 </citations>
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216 </tool>