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1 <tool id="GSAR" name="GSAR" version="0.1.0">
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2 <description>A set of multivariate statistical tests for self-contained gene set analysis</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.24.0">bioconductor-GSAR</requirement>
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6 <requirement type="package" version="1.52.1">bioconductor-GSEABase</requirement>
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7 <requirement type="package" version="1.20.3">r-getopt</requirement>
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8 </requirements>
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11 Rscript '$__tool_directory__/GSAR.R'
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12 --expr_file '$expression_data_file'
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13 --geneSet_file '$geneSet'
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14 --design_file '$desigin'
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15 --min_size '$adv.min_size'
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16 --max_size '$adv.max_size'
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17 --test_method '$method'
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18 --nperm_number '$adv.perm_num'
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19 --threshold_value '$MST.threshold'
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20 --cor_method '$MST.cor_method'
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21 --GSAR_output_p_value '$GSAR_p_value_for_the_geneSet'
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22 --GSAR_output_plot '$GSAR_Significant_pathway_plot'
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23 ]]></command>
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24
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25 <inputs>
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26 <param name="expression_data_file" type="data" format="CSV" label="Expression data file" help="A csv file containing a matrix of expression values where rows correspond to genes (symbol ID) and columns correspond to samples."/>
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27 <param name="desigin" type="data" format="CSV" label="Design" help="A csv file containing two columns corresponding to samples, one is 'group' (which sets 1 for group1 and 2 for group2), the other one is 'label' (to set group1 and group2 name/label)."/>
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28 <param name="geneSet" type="data" format="rdata" label="Gene Set" help="An `rdata` file including a geneSetCollection object with 'geneSet' as name."/>
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29 <param name="method" type="select" label="Method" help="Statistical method for testing the gene sets.">
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30 <option value="GSNCAtest" selected="true">Gene sets net correlations analysis</option>
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31 <option value="WWtest">Wald-Wolfowitz test</option>
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32 <option value="KStest">Kolmogorov-Smirnov test</option>
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33 <option value="MDtest">Mean Deviation tests</option>
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34 <option value="RKStest">Radial Kolmogorov-Smirnov test</option>
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35 <option value="RMDtest">Radial Mean Deviation test</option>
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36 </param>
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37
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38 <section name="adv" title="Advanced options">
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39 <param name="min_size" type="integer" value="10" min="5" label="Min Size for the GeneSet" help="The minimum allowed gene set size. Default value is 10." />
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40 <param name="max_size" type="integer" value="500" label="Max Size for the GeneSet" help="The maximum allowed gene set size. Default value is 500." />
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41 <param name="perm_num" type="integer" value="1000" min="100" label="Permutations number" help="Number of permutations used to estimate the null distribution of the test statistic. Default value is 1000. The minumum value is 100." />
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42 </section>
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43
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44 <section name="MST" title="Option for plotting minimum spanning trees" >
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45 <param name="threshold" type="float" value="0.05" min="0.0001" max="1" label="Threshold value" help="Threshold value to define significant geneSet for plot minimum spanning trees. Default is 0.05." />
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46 <param name="cor_method" type="select" label="Correlation coefficient statistic" help="Correlation coefficient is computed while plotting minimum spanning trees for a pathway in two conditions. Possible values are 'pearson', 'spearman' and 'kendall'. Default value is 'pearson'. " >
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47 <option value="pearson" selected="true">pearson</option>
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48 <option value="spearman">spearman</option>
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49 <option value="kendall">kendall</option>
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50 </param>
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51 </section>
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52
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53 </inputs>
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54
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55 <outputs>
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56 <data name="GSAR_p_value_for_the_geneSet" format="CSV" label="GSAR_p_value_for_the_geneSet" />
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57 <data name="GSAR_Significant_pathway_plot" format="pdf" label="GSAR_Significant_pathway_plot" />
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58 </outputs>
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59
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60 <tests>
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61 <test>
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62 <param name="expression_data_file" value="GSAR_input_p53DataSet.csv" ftype="csv" />
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63 <param name="desigin" value="GSAR_design.csv" ftype="csv" />
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64 <param name="method" value="GSNCAtest" />
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65 <section name="adv">
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66 <param name="min_size" value="10" />
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67 <param name="max_size" value="500" />
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68 <param name="perm_num" value="1000"/>
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69 </section>
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70 <section name="MST">
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71 <param name="threshold" value="0.05" />
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72 <param name="cor_method" value="pearson" />
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73 </section>
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74 <output name="GSAR_p_value_for_the_geneSet" file="GSAR_p_value_for_the_geneSet.csv" ftype="csv" />
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75 <output name="GSAR_Significant_pathway_plot" file="GSAR_Significant_pathway_plot.pdf" ftype="pdf" />
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76 </test>
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77 </tests>
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78
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79 <help><![CDATA[
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80
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81 .. class:: infomark
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82
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83 **What it does**
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84
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85 **GSAR (Gene Set Analysis in R)** is an R package which provides a set of multivariate statistical tests for self-contained gene set analysis (GSA). GSAR consists of two-sample multivariate nonparametric statistical methods testing a null hypothesis against specific alternative hypotheses, such as differences in mean (shift), variance (scale) or correlation structure. It also offers a graphical visualization tool for the correlation networks obtained from expression data to examine the change in the net correlation structure of a gene set between two conditions based on the minimum spanning trees.
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86
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87 ---------
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88
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89 =========
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90 **Input**
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91 =========
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92
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93 **Gene expression data**
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94
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95 The input is a csv file including a matrix of expression values where rows correspond to genes and columns correspond to samples.
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96 Recommended gene id is `Symbol ID`.
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97
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98 **Design**
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99
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100 A csv file that has two columns correspond to samples, one is `'group'` (which sets 1 for group1 and 2 for group2), the other one is `'label'` (to set group1 and group2 name/label).
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101
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102 Example:
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103
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104 ======= ======= =========
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105 sample group label
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106 ======= ======= =========
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107 WT1 1 control
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108 WT2 1 control
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109 WT3 1 control
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110 ... ... ...
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111 MUT31 2 test
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112 MUT32 2 test
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113 MUT33 2 test
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114 ======= ======= =========
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115
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116 **Gene Sets**
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117
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118 **Gene Sets** is an `rdata` file including a `geneSet` variable that is a `geneSetCollection` object built by the `GSEABase` bioconductor package. You can use the **GeneSet from Msigdb/KEGG** tool to get this file. You must pay attention to set the same gene id type as in the gene expression dataset.
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119
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120 **Method**
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121
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122 Statistical method to use for testing the gene sets. Must be one of *GSNCA (Gene sets net correlations analysis)*, Wald-Wolfowitz test, Kolmogorov-Smirnov test, Mean Deviation test, Radial Kolmogorov-Smirnov test and Radial Mean Deviation test.
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123
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124 **Min Size for the Gene Set**
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125
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126 The minimum allowed gene set size. Default value is 10.
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127
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128 **Max Size for the Gene Set**
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129
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130 The maximum allowed gene set size. Default value is 500.
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131
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132 **Permutations number**
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133
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134 Number of permutations used to estimate the null distribution of the test statistic. Default value is 1000. The minumum value is 100.
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135
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136 **Threshold value**
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137
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138 Threshold value to define significant geneSet for plotting minimum spanning trees. Default as 0.05.
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139
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140 **Correlation coefficient statistic**
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141
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142 Correlation coefficient is computed to plot minimum spanning trees for a pathway in two conditions. Possible values are 'pearson' (default), 'spearman' and 'kendall'. Default value is 'pearson'.
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143
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144 ---------
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145
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146 ==========
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147 **Output**
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148 ==========
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149
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150 **1. A csv file containing the P-values of all gene sets**
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151
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152 Example
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153
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154 ========= ==========
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155 geneSet p_value
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156 ========= ==========
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157 pathway_1 0.007
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158 pathway_2 0.008
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159 pathway_3 0.009
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160 pathway_4 0.010
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161 ... ...
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162 pathway_n 0.999
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163 ========= ==========
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164
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165 **2. Plot of minimum spanning trees for significant gene sets in two conditions**
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166
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167 ]]></help>
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168
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169 <citations>
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170 <citation type="doi">10.1186/s12859-017-1482-6</citation>
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171 </citations>
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172
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173 </tool> |
