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1 <tool id="methylGSA" name="methylGSA" version="0.1.0" python_template_version="3.5">
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2 <description>Gene Set Analysis for DNA Methylation data</description>
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3
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4 <requirements>
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5 <requirement type="package" version="0.6.0">bioconductor-IlluminaHumanMethylationEPICanno.ilm10b4.hg19</requirement>
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6 <requirement type="package" version="0.6.0">bioconductor-IlluminaHumanMethylation450kanno.ilmn12.hg19</requirement>
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7 <requirement type="package" version="1.8.0">bioconductor-methylGSA</requirement>
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8 <requirement type="package" version="1.20.3">r-getopt</requirement>
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9 </requirements>
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10
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11 <command detect_errors="exit_code"><![CDATA[
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12 Rscript '$__tool_directory__/methylGSA.R'
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13 --data_file '$data_file'
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14 --test_method '$method'
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15 --array_type '$array_type'
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16 --group '$Group'
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17 --GS_list '$geneset'
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18 --minsize '$minSize'
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19 --maxsize '$maxSize'
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20 --result '$gsa_result'
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21
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22 ]]></command>
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23
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24 <inputs>
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25 <param name="data_file" type="data" format="txt" label="CpG IDs and their p-value" help="A text file with two columns: The CpG IDs and their p-values." />
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26 <param name="array_type" type="select" label="Array_type" help="450K or EPIC." >
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27 <option value="450K">450K</option>
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28 <option value="EPIC">EPIC</option>
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29 </param>
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30 <param name="Group" type="select" label="Group" help="See help for more details.">
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31 <option value="all">all</option>
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32 <option value="body">body</option>
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33 <option value="promoter1">promoter1</option>
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34 <option value="promoter2">promoter2</option>
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35 </param>
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36 <param name="method" type="select" label="Test method" display="radio" help="See help for more details." >
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37 <option value="methylglm">methylglm</option>
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38 <option value="gometh">gometh</option>
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39 <option value="RRA_ORA">RRA(ORA)</option>
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40 <option value="RRA_GSEA">RRA(GSEA)</option>
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41 </param>
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42 <param name="geneset" type="select" label="Gene sets" help="Select gene sets to test." >
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43 <option value="GO">Gene Ontology</option>
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44 <option value="KEGG">KEGG</option>
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45 <option value="Reactome">Reactome</option>
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46 </param>
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47
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48 <param name="minSize" type="integer" label="Minimum gene set size" value="15" min="1" max="1000" help="Gene sets with less than this number of elements will not be included in the analysis." />
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49 <param name="maxSize" type="integer" label="Maximum gene set size" value="500" min="1" max="1000" help="Gene sets with more than this number of elements will not be included in the analysis." />
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50
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51 </inputs>
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52
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53 <outputs>
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54 <data name="gsa_result" format="csv" label="methylGSA_result" />
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55 </outputs>
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56
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57 <tests>
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58 <test>
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59 <param name="data_file" value="cpg.csv" ftype="txt" />
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60 <param name="array_type" value="450K"/>
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61 <param name="Group" value="all" />
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62 <param name="method" value="methylglm" />
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63 <param name="geneset" value="GO" />
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64 <param name="minSize" value="15" />
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65 <param name="maxSize" value="500" />
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66 <output name="gsa_result" file="methylGSA_result.csv" ftype="csv" />
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67 </test>
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68 </tests>
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69
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70 <help><![CDATA[
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71
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72 .. class:: infomark
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73
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74 **What it does**
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75
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76 **methylGSA** is a tool for gene set testing with length bias adjustment for DNA methylation data.
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77 It allows users to identify enriched or over-represented gene sets or pathways from the Gene
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78 Ontology, KEGG and Reactome databases.
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79
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80 -------
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81
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82 =========
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83 **Input**
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84 =========
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85
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86 **CpG IDs and their p-value**
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87
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88 Users are expected to upload a txt file with two columns: The fist column with the CpG IDs, and the second column with the p-values correspond to the CpGs. For example:
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89
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90 =========== ===========
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91 cg13869341 0.307766
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92 cg14008030 0.257672
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93 cg12045430 0.552322
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94 cg20826792 0.056383
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95 cg00381604 0.468549
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96 cg20253340 0.483770
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97 cg21870274 0.812402
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98 =========== ===========
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99
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100 Files should be no more than 100MB.
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101
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102 **array_type**
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103
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104 `450K`: Illumina 450 K Beadchip
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105
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106 `EPIC`: Illumina EPIC Beadchip
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107
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108 **Group**
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109
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110 **Group** defines the type of CpG to be considered by the `methylRRA` or `methylglm` functions. By default,
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111 group is set to `all`, which means that all CpGs are considered regardless of their gene group.
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112 If group is set to `body`, only CpGs on gene body will be considered. If group is `promoter1`
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113 or `promoter2`, only CpGs on promoters will be considered.
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114 Based on the annotation in IlluminaHumanMethylation450kanno.ilmn12.hg19
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115 and IlluminaHumanMethylationEPICanno.ilm10b4.hg19, `body`, `promoter1` and `promoter2` are defined as:
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116
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117 * body: CpGs whose gene group correspond to “Body” or “1stExon”
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118 * promoter1: CpGs whose gene group correspond to “TSS1500” or “TSS200”
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119 * promoter2: CpGs whose gene group correspond to “TSS1500”, “TSS200”, “1stExon”, or “5’UTR”
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120
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121 **Test method**
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122
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123 * methylglm: Implement logistic regression adjusting for number of probes in enrichment analysis
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124 * gometh: Gene ontology testing for Illumina methylation array data
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125 * RRA(ORA): Enrichment analysis with ORA method after adjusting multiple p-values of each gene by Robust Rank Aggregation
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126 * RRA(GSEA): Enrichment analysis with GSEA method after adjusting multiple p-values of each gene by Robust Rank Aggregation
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127
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128 **Gene sets tested**
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129
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130 * Gene Ontology: http://www.geneontology.org
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131 * KEGG (Kyoto Encyclopedia of Genes and Genomes): https://www.genome.jp/kegg/
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132 * Reactome: https://reactome.org
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133
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134 ==========
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135 **Output**
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136 ==========
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137
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138 **methylGSA_result**
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139 This file is a csv file which contains gene set tests results.
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140
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141 ]]></help>
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142
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143 <citations>
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144 <citation type="doi">10.1093/bioinformatics/bty892</citation>
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145 </citations>
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146
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147 </tool>
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