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1 <tool id="ReactomePA" name="ReactomePA" version="0.1.0">
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2 <description>Reactome Pathway Analysis</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.20.3">r-getopt</requirement>
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6 <requirement type="package" version="1.34.0">bioconductor-ReactomePA</requirement>
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7 <requirement type="package" version="3.12.0">bioconductor-org.Hs.eg.db</requirement>
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8 </requirements>
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9
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10 <command detect_errors="exit_code" interpreter="Rscript --vanilla"><![CDATA[
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11 $__tool_directory__/ReactomePA.R
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12 -g '$gene_list_file'
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13 -s '$Significant_Reactome_Pathway_result'
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14
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15 -o '$organism'
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16
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17 -p '$adv.pvalueCutoff'
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18 -w '$adv.pAdjustMethod'
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19 #if $adv.convertId=="TRUE":
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20 -c
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21 #end if
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22 -i '$adv.minGSSize'
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23 -a '$adv.maxGSSize'
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24 ]]></command>
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25
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26 <inputs>
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27 <param type="data" name="gene_list_file" format="csv" label="Differentially expressed gene list" help="A csv file including a DEgenes column, that is, the Entrez ID of all differentially expressed genes." />
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28 <param type="select" name="organism" label="Organism" help="Choose organism. Only human, rat, mouse, celegans, yeast, zebrafish and fly are included.">
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29 <option value="human" selected="True">human (H sapiens)</option>
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30 <option value="rat">rat (R norvegicus)</option>
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31 <option value="mouse">house mouse (M musculus)</option>
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32 <option value="celegans">roundworm (C elegans)</option>
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33 <option value="yeast">yeast (S cerevisiae)</option>
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34 <option value="zebrafish">zebrafish (D rerio)</option>
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35 <option value="fly">fruit fly (D melanogaster)</option>
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36 </param>
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37
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38 <section name="adv" title="Advanced Options" expanded="false">
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39 <param type="float" name="pvalueCutoff" value="0.05" min="0.00" max="1.00" label="P-value threshold" help="This is the cutoff p-value to determine significant enrichment of a pathway. Default is 0.05."/>
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40 <param type="select" name="pAdjustMethod" label="Method to adjust pathway p-values for multiple testing" help="Choose one method to adjust pathway p-values.">
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41 <option value="BH" selected="True">BH</option>
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42 <option value="holm">holm</option>
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43 <option value="hochberg">hochberg</option>
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44 <option value="hommel">hommel</option>
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45 <option value="bonferroni">bonferroni</option>
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46 <option value="BY">BY</option>
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47 <option value="fdr">fdr</option>
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48 <option value="none">none</option>
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49 </param>
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50 <param type="boolean" name="convertId" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Convert gene ID to SYMBOL" help="Select Yes if you want to convert entrez gene IDs to gene names (see the Help section below). Default: No." />
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51 <param type="integer" name="minGSSize" value="10" label="Minimum size of each geneSet" help="Gene sets with less genes than this value will be ignored."/>
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52 <param type="integer" name="maxGSSize" value="500" label="Maximum size of each geneSet" help="Gene sets with more genes than this value will be ignored." />
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53 </section>
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54
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55 </inputs>
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56
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57 <outputs>
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58 <data name="Significant_Reactome_Pathway_result" format="csv" label="Significant_Reactome_Pathway_result" />
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59 </outputs>
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60
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61 <tests>
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62 <test>
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63 <param name="gene_list_file" value="Different_expression_gene.csv" ftype="csv" />
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64 <param name="organism" value="human"/>
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65 <param name="minGSSize" value="15"/>
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66 <param name="maxGSSize" value="200"/>
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67 <param name="pvalueCutoff" value="0.06"/>
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68 <param name="pAdjustMethod" value="holm"/>
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69 <param name="input7" value="true"/>
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70 <output name="Significant_Reactome_Pathway_result" file="t1.csv" ftype="csv" />
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71 </test>
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72 </tests>
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73
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74 <help><![CDATA[
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75
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76 .. class:: infomark
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77
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78 **What it does**
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79
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80 Reactome_ is a free, open-source, curated and peer-reviewed pathway database.
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81 Their goal is to provide intuitive bioinformatics tools for the visualization,
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82 interpretation and analysis of pathway knowledge.
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83
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84 .. _Reactome: https://reactome.org
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85
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86 **ReactomePA** is a tool to enrich Significant Reactome Pathways with a list of differentially expressed genes.
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87
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88 This tool uses the function `enrichPathway` in the ReactomePA_ package.
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89
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90 .. _ReactomePA: http://www.bioconductor.org/packages/release/bioc/html/ReactomePA.html
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91
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92 ---------
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93
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94 ==========
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95 **Inputs**
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96 ==========
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97
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98 Basic Options
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99 --------------
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100
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101 **Differentially expressed gene list**
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102
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103 This tool requires a csv file which has a `DEgenes` column containing the entrez gene ID of all differentially expressed genes.
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104
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105 Example:
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106
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107 ========== ===
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108 DEgenes
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109 ========== ===
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110 4312
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111 8318
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112 10874
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113 55143
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114 55388
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115 991
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116 ========== ===
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117
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118 **Organism**
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119
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120 Choose the right organism for your data. Only human, rat, mouse, celegans, yeast, zebrafish and fly are included.
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121
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122 Advanced Options
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123 -----------------
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124
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125 **P-value threshold**
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126
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127 This is the cutoff p-value to determine significant enrichment of a pathway. Default is 0.05.
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128
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129 **Method to adjust pathway p-values for multiple testing**
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130
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131 Choose one method to adjust pathway p-values. Included methods are: `"BH"`, `"holm"`, `"hochberg"`, `"hommel"`, `"bonferroni"`, `"BY"`, `"fdr"` and `"none"`. Default is `"BH"`.
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132
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133 **Convert gene ID to SYMBOL**
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134
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135 If you want to convert entrez gene ID to gene SYMBOL name, choose Yes. Default: No.
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136
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137 **Minimum and maximum size of each geneSet**
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138
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139 Set minimum and maximum size of each gene set to be included in the analysis. Default are 10 and 500.
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140
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141 ------
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142
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143 ==========
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144 **Output**
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145 ==========
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146
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147 A csv file including all enriched pathways.
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148
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149 Example - **Single Count Matrix**:
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150
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151 =============== =============================================== =========== ===========
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152 ID Description GeneRatio BgRatio
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153 =============== =============================================== =========== ===========
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154 R-HSA-69618 Mitotic Spindle Checkpoint 22/326 113/10704
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155 R-HSA-2500257 Resolution of Sister Chromatid Cohesion 23/326 126/10704
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156 R-HSA-141424 Amplification of signal from the kinetochores 20/326 96/10704
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157 R-HSA-9648025 EML4 and NUDC in mitotic spindle formation 20/326 117/10704
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158 R-HSA-5663220 RHO GTPases Activate Formins 21/326 140/10704
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159 =============== =============================================== =========== ===========
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160
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161
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162 ]]></help>
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163
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164 <citations>
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165 <citation type="doi">10.1039/c5mb00663e</citation>
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166 </citations>
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167
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168 </tool>
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