Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.xml @ 11:3ddc1f78773d draft

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author proteore
date Fri, 28 Jun 2019 05:11:15 -0400
parents 2138e0035e57
children d4dd1c242a87
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1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.06.27">
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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="3.4.1">R</requirement>
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5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
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6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
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7 <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement-->
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8 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
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9 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
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10 <requirement type="package" version="1.38.0">goprofiles</requirement>
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11
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12 </requirements>
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13 <stdio>
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14 <exit_code range="1:" />
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15 </stdio>
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16 <command><![CDATA[
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17 Rscript $__tool_directory__/goprofiles.R
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18 #if $input.ids == "text"
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19 --input_type="text"
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20 --input="$input.text"
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21 #else
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22 --input_type="file"
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23 --input="$input.file"
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24 --ncol="$input.ncol"
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25 --header="$input.header"
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26 #end if
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27
1
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28 --id_type="$input.id_type"
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29 --onto_opt="$onto_opt"
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30 --plot_opt="$plot_opt"
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31 --level="$level"
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32 --per="$per"
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33 --title="$title"
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34 --duplicate="$duplicate"
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35 --text_output="$text_output"
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36 --species="$species" > $log
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37
0
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38 ]]></command>
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39 <inputs>
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40 <conditional name="input" >
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41 <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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42 <option value="text">Copy/paste your IDs</option>
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43 <option value="file" selected="true">Input file containing your IDs</option>
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44 </param>
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45 <when value="text" >
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46 <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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47 <sanitizer>
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48 <valid initial="string.printable">
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49 <remove value="&apos;"/>
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50 </valid>
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51 <mapping initial="none">
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52 <add source="&apos;" target="__sq__"/>
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53 </mapping>
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54 </sanitizer>
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55 </param>
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56 <param name="id_type" type="select" label="Select type of IDs list" >
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57 <option value="Entrez">Entrez Gene ID</option>
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58 <option value="UniProt">UniProt Accession number</option>
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59 </param>
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60 </when>
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61 <when value="file" >
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62 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
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63 <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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64 <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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65 </param>
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66 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
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67 <param name="id_type" type="select" label="Select type of IDs list" >
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68 <option value="Entrez">Entrez Gene ID</option>
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69 <option value="UniProt">Uniprot Accession number</option>
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70 </param>
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71 </when>
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72 </conditional>
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73 <param name="duplicate" type="boolean" checked="true" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
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74 <param name="species" type="select" label="Species">
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75 <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
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76 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
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77 <!--option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option-->
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78 </param>
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79 <param type="select" name="onto_opt" label="Select GO terms category" multiple="True" display="checkboxes" optional="false" >
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80 <option value="CC">Cellular Component (CC)</option>
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81 <option value="MF">Molecular Function (MF)</option>
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82 <option value="BP">Biological Process (BP)</option>
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83 </param>
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84 <param type="select" name="level" label="Ontology level (the higher this number, the deeper the GO level)" >
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85 <option value="1">1</option>
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86 <option value="2" selected="True">2</option>
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87 <option value="3">3</option>
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88 <option value="4">4</option>
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89 <option value="5">5</option>
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90 <option value="6">6</option>
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91 </param>
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92 <param type="boolean" name="per" label="Plot absolute frequencies?" truevalue="TRUE" falsevalue="FALSE" />
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93 <param type="text" name="title" label="Enter title of your figure">
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94 <sanitizer invalid_char=''>
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95 <valid initial="string.printable">
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96 <remove value="&apos;"/>
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97 <remove value="/"/>
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98 </valid>
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99 <mapping>
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100 <add source="&#x20;" target=""/>
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101 </mapping>
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102 </sanitizer>
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103 </param>
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104 <param type="select" name="plot_opt" label="Plot file format">
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105 <option value="PNG" selected="True">png</option>
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106 <option value="JPEG">jpeg</option>
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107 <option value="PDF">pdf</option>
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108 </param>
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109
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110 </inputs>
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111 <outputs>
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112 <data name="log" format="tsv" label="goProfiles log" />
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113 <collection type="list" label="goProfiles text files" name="text_output">
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114 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tsv"/>
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115 </collection>
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116 <collection type="list" label="goProfiles diagram output" name="output" >
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117 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
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118 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" />
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119 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" />
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120 </collection>
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121 </outputs>
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122 <tests>
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123 <test>
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124 <conditional name="input">
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125 <param name="ids" value="file" />
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126 <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
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127 <param name="ncol" value="c1" />
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128 <param name="header" value="true" />
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129 <param name="id_type" value="UniProt" />
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130 </conditional>
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131 <param name="duplicate" value="false"/>
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132 <param name="onto_opt" value="CC,MF,BP" />
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133 <param name="level" value="2" />
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134 <param name="per" value="true" />
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135 <param name="title" value="Test" />
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136 <param name="plot_opt" value="PDF" />
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137 <output_collection name="output" type="list" >
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138 <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/>
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139 <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/>
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140 <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/>
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141 </output_collection>
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142 <output name="log" file="GO_Profile_text_output.tsv"/>
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143 </test>
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144 </tests>
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145 <help><![CDATA[
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146
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147 **Description**
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148
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149 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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150 number of identifiers having a hit in each category of this level.
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151
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152 -----
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153
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154 **Input**
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155
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156 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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157 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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158
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159 .. class:: warningmark
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160
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161 In copy/paste mode, the number of IDs considered in input is limited to 5000.
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162
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163 -----
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164
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165 **Parameters**
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166
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167 "Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon)
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168
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169 "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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170
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171 "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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172
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173 -----
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174
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175 **Ouput**
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176
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177 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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178
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179 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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180
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181 -----
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182
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183 .. class:: infomark
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184
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185 Packages used:
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186 - bioconductor-org.hs.eg.db v3.5.0
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187 - bioconductor-org.mm.eg.db v3.5.0
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188 - bioconductor-annotationdbi v1.40.0
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189 - bioconductor-biobase v2.98.0
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190 - goprofiles v1.38.0
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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>