annotate goseq.xml @ 4:ae39895af5fe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0798278a90c08228a386516881680b328fc33f0c
author iuc
date Sun, 30 Sep 2018 09:27:05 -0400
parents 783e8b70b047
children bbcf5f7f2af2
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1 <tool id="goseq" name="goseq" version="1.30.1">
0
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2 <description>tests for overrepresented gene categories</description>
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3 <requirements>
3
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4 <requirement type="package" version="1.6.0">r-optparse</requirement>
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5 <requirement type="package" version="1.30.0">bioconductor-goseq</requirement>
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6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
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7 <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement>
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8 <requirement type="package" version="3.5.0">bioconductor-org.dr.eg.db</requirement>
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9 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
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10 <requirement type="package" version="0.7.6">r-dplyr</requirement>
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11 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
0
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12 </requirements>
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13 <stdio>
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14 <regex match="Execution halted"
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15 source="both"
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16 level="fatal"
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17 description="Execution halted." />
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18 <regex match="Error in"
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19 source="both"
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20 level="fatal"
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21 description="An undefined error occured, please check your input carefully and contact your administrator." />
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22 <regex match="Fatal error"
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23 source="both"
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24 level="fatal"
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25 description="An undefined error occured, please check your input carefully and contact your administrator." />
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26 </stdio>
2
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27 <version_command><![CDATA[
3
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28 echo $(R --version | grep version | grep -v GNU)", goseq version" $(R --vanilla --slave -e "library(goseq); cat(sessionInfo()\$otherPkgs\$goseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
2
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29 ]]></version_command>
0
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30 <command><![CDATA[
2
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31 Rscript '$__tool_directory__/goseq.r'
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32
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33 --dge_file '$dge_file'
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34 --length_file '$length_file'
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35
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36 #if $categorySource.catSource == 'getgo':
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37 --genome $categorySource.genome
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38 --gene_id $categorySource.gene_id
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39 --fetch_cats '$categorySource.fetchcats'
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40 #elif $categorySource.catSource == 'history':
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41 --category_file '$categorySource.category_file'
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42 #end if
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43
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44 #if $methods['wallenius']:
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45 --wallenius_tab '$wallenius_tab'
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46 #end if
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47 #if $methods['hypergeometric']:
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48 --nobias_tab '$nobias_tab'
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49 #end if
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50 --repcnt '$methods.repcnt'
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51 --sampling_tab '$sampling_tab'
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52
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53 --make_plots '$out.make_plots'
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54 --length_bias_plot '$length_bias_plot'
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55 --sample_vs_wallenius_plot '$sample_vs_wallenius_plot'
3
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56
2
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57 --rdata '$out.rdata_out'
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58 --p_adj_method '$adv.p_adj_method'
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59 --use_genes_without_cat '$adv.use_genes_without_cat'
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60
3
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61 #if $out.topgo_plot:
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62 --top_plot '$out.topgo_plot'
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63 #end if
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64
0
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65 ]]></command>
2
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66
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67 <!-- Input Files-->
0
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68 <inputs>
2
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69 <param name="dge_file" type="data" format="tabular" label="Differentially expressed genes file" help="A tabular file with Gene IDs in the first column, and True or False in the second column. True means a gene is differentially expressed. See Help section for details."/>
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70 <param name="length_file" type="data" format="tabular" label="Gene lengths file" help="You can calculate the gene lengths using featureCounts or the Gene length and GC content tool."/>
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71 <conditional name="categorySource">
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72 <param name="catSource" type="select" format="tabular" label="Gene categories" help="You can obtain a mapping of genes to categories (for some genomes only) or you can provide your own category file.">
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73 <option value="getgo" selected="true">Get categories</option>
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74 <option value="history">Use a category file from history</option>
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75 </param>
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76 <when value="getgo">
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77 <param name="genome" type="select" label="Select a genome to use">
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78 <option value="hg38">Human (hg38)</option>
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79 <option value="mm10">Mouse (mm10)</option>
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80 <option value="dm6">Fruit fly (dm6)</option>
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81 <option value="danRer10">Zebrafish (danRer10)</option>
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82 </param>
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83 <param name="gene_id" type="select" label="Select Gene ID format" help="Supported Gene IDs to automatically fetch categories should either be Entrez, Ensembl, or gene symbols.">
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84 <option value="ensGene">Ensembl Gene ID</option>
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85 <option value="knownGene">Entrez Gene ID</option>
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86 <option value="geneSymbol">Gene Symbol</option>
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87 </param>
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88 <param name="fetchcats" type="select" multiple="True" display="checkboxes" label="Select one or more categories" help="By default, goseq tests all three major Gene Ontology branches; Cellular Component, Biological Process and Molecular Function. However, it is possible to limit testing to any combination and/or to also use KEGG pathways.">
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89 <option value="GO:CC" selected="True">GO: Cellular Component</option>
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90 <option value="GO:BP" selected="True">GO: Biological Process</option>
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91 <option value="GO:MF" selected="True">GO: Molecular Function</option>
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92 <option value="KEGG">KEGG</option>
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93 </param>
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94 </when>
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95 <when value="history">
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96 <param name="category_file" type="data" format="tabular" label="Gene category file"/>
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97 </when>
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98 </conditional>
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99
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100 <!-- Method Options -->
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101 <section name="methods" title="Method Options">
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102 <param name="wallenius" type="boolean" checked="true" label="Use Wallenius method" help="See help for details. Default: Yes" />
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103 <param name="hypergeometric" type="boolean" checked="false" label="Use Hypergeometric method" help="Does not use gene length information. See help for details. Default: No" />
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104 <param name="repcnt" type="integer" size="3" min="0" max="10000" value="0" label="Sampling number" help="Number of random samples to be calculated when sampling is used. Set to 0 to not do sampling. Larger values take a long time. Default: 0" />
0
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105 </section>
2
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106
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107 <!-- Output Options -->
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108 <section name="out" title="Output Options">
3
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109 <param name="topgo_plot" type="boolean" checked="false" label="Output Top GO terms plot?" help="Output a PDF plot of the Top 10 over-represented GO terms. Default: No" />
2
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110 <param name="make_plots" type="boolean" checked="false" label="Produce diagnostic plots?" help="This will produce the length bias (PWF) plot. If both sampling and wallenius methods are selected, it will also produce a plot comparing their p-values. These plots may help you compare the different p-value estimation methods that goseq can use. Default: No" />
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111 <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No" />
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112 </section>
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113
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114 <!-- Advanced Options -->
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115 <section name="adv" title="Advanced Options">
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116 <param name="p_adj_method" type="select" label="Select a method for multiple hypothesis testing correction">
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117 <option value="BH" selected="True">Benjamini-Hochberg [FDR] (1995)</option>
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118 <option value="holm">Holm (1979)</option>
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119 <option value="hommel">Hommel (1988)</option>
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120 <option value="hochberg">Hochberg (1988)</option>
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121 <option value="bonferroni">Bonferroni</option>
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122 <option value="BY">Benjamini - Yekutieli (2001)</option>
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123 </param>
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124 <param name="use_genes_without_cat" type="boolean" checked="false" label="Count genes without any category?" help="For example, a large number of genes may have no GO term annotated. If this option is set to No, those genes will be ignored in the calculation of p-values. If this option is set to Yes, then these genes will count towards the total number of genes outside the category being tested. This was the default behaviour for version 1.15.1 and earlier. Default: No"/>
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125 </section>
0
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126 </inputs>
2
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127
0
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128 <outputs>
2
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129 <data name="wallenius_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Wallenius method">
3
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130 <filter>methods['wallenius']</filter>
0
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131 </data>
2
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132 <data name="sampling_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Sampling method">
0
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133 <filter>methods['repcnt'] != 0</filter>
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134 </data>
2
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135 <data name="nobias_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Hypergeometric method">
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136 <filter>methods['hypergeometric']</filter>
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137 </data>
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138 <data name="length_bias_plot" format="pdf" label="${tool.name} on ${on_string}: Length bias plot">
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139 <filter>out['make_plots']</filter>
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140 </data>
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141 <data name="sample_vs_wallenius_plot" format="pdf" label="${tool.name} on ${on_string}: Sampling vs Wallenius P-values plot">
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142 <filter>methods['repcnt'] != 0</filter>
0
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143 <filter>methods['wallenius']</filter>
2
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144 <filter>out['make_plots']</filter>
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145 </data>
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146 <data name="rdata" format="rdata" from_work_dir="goseq_analysis.RData" label="${tool.name} on ${on_string}: RData file">
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147 <filter>out['rdata_out']</filter>
0
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148 </data>
3
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149 <data name="top_plot" format="pdf" from_work_dir="top10.pdf" label="${tool.name} on ${on_string}: Top over-represented GO terms plot">
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150 <filter>methods['wallenius']</filter>
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151 <filter>out['topgo_plot']</filter>
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152 </data>
0
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153 </outputs>
2
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154
0
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155 <tests>
3
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156 <!-- Ensure top plot is output -->
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157 <test expect_num_outputs="2">
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158 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
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159 <param name="length_file" value="gene_length.tab" ftype="tabular" />
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160 <param name="catSource" value="history" />
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161 <param name="category_file" value="category.tab" ftype="tabular" />
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162 <param name="use_genes_without_cat" value="true" />
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diff changeset
163 <param name="topgo_plot" value="true" />
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
164 <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/>
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
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165 </test>
2
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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166 <!-- Ensure Wallenius table is output -->
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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167 <test expect_num_outputs="1">
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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168 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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169 <param name="length_file" value="gene_length.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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170 <param name="catSource" value="history" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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171 <param name="category_file" value="category.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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172 <param name="use_genes_without_cat" value="true" />
3
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
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173 <output name="wallenius_tab">
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
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174 <assert_contents>
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
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175 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" />
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
176 <has_text_matching expression="GO:0000278.*0.01" />
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
177 </assert_contents>
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
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178 </output>
2
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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179 </test>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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180 <!-- Ensure getting GO categories works -->
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
181 <test expect_num_outputs="1">
0
ade933eff007 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
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diff changeset
182 <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
ade933eff007 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff changeset
183 <param name="length_file" value="gene_length.tab" ftype="tabular"/>
2
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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184 <param name="catSource" value="getgo" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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185 <param name="genome" value="hg38" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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186 <param name="gene_id" value="ensGene" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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187 <param name="use_genes_without_cat" value="true" />
3
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
188 <output name="wallenius_tab">
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
189 <assert_contents>
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
190 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" />
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
191 <has_text_matching expression="GO:0005576.*5.2" />
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
192 </assert_contents>
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
193 </output>
2
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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194 </test>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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195 <!-- Ensure getting GO categories for another genome (zebrafish) works -->
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
196 <test expect_num_outputs="1">
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
197 <param name="dge_file" value="dge_list_zf.tab" ftype="tabular"/>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
198 <param name="length_file" value="gene_length_zf.tab" ftype="tabular"/>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
199 <param name="catSource" value="getgo" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
200 <param name="genome" value="danRer10"/>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
201 <param name="gene_id" value="ensGene" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
202 <param name="use_genes_without_cat" value="true" />
3
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
203 <output name="wallenius_tab">
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
204 <assert_contents>
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
205 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" />
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
206 <has_text_matching expression="GO:0031324.*0.08" />
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
207 </assert_contents>
783e8b70b047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 2
diff changeset
208 </output>
2
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
209 </test>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
210 <!-- Ensure length bias plot works -->
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
211 <test expect_num_outputs="2">
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
212 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
213 <param name="length_file" value="gene_length.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
214 <param name="catSource" value="history" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
215 <param name="category_file" value="category.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
216 <param name="make_plots" value="true" />
0
ade933eff007 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff changeset
217 <param name="use_genes_without_cat" value="true" />
2
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
218 <output name="length_bias_plot" ftype="pdf" file="length_bias_plot.pdf" compare="sim_size" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
219 </test>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
220 <!-- Ensure hypergeometric works -->
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
221 <test expect_num_outputs="2">
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
222 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
223 <param name="length_file" value="gene_length.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
224 <param name="catSource" value="history" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
225 <param name="category_file" value="category.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
226 <param name="use_genes_without_cat" value="true" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
227 <param name="hypergeometric" value="true" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
228 <output name="nobias_tab" file="nobias.tab" compare="contains" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
229 </test>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
230 <!-- Ensure sampling vs wallenius works -->
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
231 <test expect_num_outputs="4">
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
232 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
233 <param name="length_file" value="gene_length.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
234 <param name="catSource" value="history" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
235 <param name="category_file" value="category.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
236 <param name="use_genes_without_cat" value="true" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
237 <param name="make_plots" value="true" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
238 <param name="repcnt" value="1000" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
239 <output name="sampling_tab" file="samp.tab" compare="sim_size" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
240 <output name="length_bias_plot" ftype="pdf" file="length_bias_plot.pdf" compare="sim_size" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
241 <output name="sample_vs_wallenius_plot" ftype="pdf" file="sample_vs_wallenius_plot.pdf" compare="sim_size" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
242 </test>
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
243 <!-- Ensure RData output works -->
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
244 <test expect_num_outputs="2">
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
245 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
ab492df30cdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
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246 <param name="length_file" value="gene_length.tab" ftype="tabular" />
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247 <param name="catSource" value="history" />
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248 <param name="category_file" value="category.tab" ftype="tabular" />
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249 <param name="use_genes_without_cat" value="true" />
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250 <param name="rdata_out" value="true" />
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251 <output name="rdata" file="goseq_analysis.RData" compare="sim_size" />
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252 </test>
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253 </tests>
2
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254
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255 <help><![CDATA[
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256
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257 .. class:: infomark
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258
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259 **What it does**
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260
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261 `Gene Ontology`_ (GO) analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. This tool provides methods for performing GO analysis of RNA-seq data, taking length bias into account. The methods and software used by goseq are equally applicable to other category based tests of RNA-seq data, such as KEGG_ pathway analysis.
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262
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263 Options map closely to the excellent goseq manual_.
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264
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265 -----
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266
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267 **Inputs**
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268
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269 *Differentially expressed genes file*
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270
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271 goseq needs a tabular file containing information on differentially expressed genes. This should contain all genes assayed in the RNA-seq experiment. The file should have two columns with an optional header row. The first column should contain the Gene IDs, which must be unique within the file and not repeated. The second column should contain True or False. True means the gene should count as differentially expressed, False means it is not differentially expressed. You can use the "Compute an expression on every row" tool to create a True / False column for your dataset.
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272
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273 Example:
0
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274
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275 =============== =====
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276 ENSG00000236824 False
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277 ENSG00000162526 False
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278 ENSG00000090402 True
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279 ENSG00000169188 False
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280 ENSG00000124103 False
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281 =============== =====
0
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282
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283 *Gene lengths file*
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284
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285 goseq needs information about the length of a gene to correct for potential length bias in differentially expressed genes using a Probability Weight Function (PWF). The PWF can be thought of, as a function which gives the probability that a gene will be differentially expressed, based on its length alone. The gene length file should have two columns with an optional header row. The first column should contain the Gene IDs, and the second column should contain the gene length in bp. If length data is unavailable for some genes, that entry should be set to NA. The goseq authors recommend using the gene lengths obtained from upstream summarization programs, such as **featureCounts**, if provided. Alternatively, the **Gene length and GC content** tool can produce such a file.
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286
2
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287 Example:
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288
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289 =============== =====
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290 ENSG00000236824 13458
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291 ENSG00000162526 2191
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292 ENSG00000090402 6138
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293 ENSG00000169188 3245
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294 ENSG00000124103 1137
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295 =============== =====
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296
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297 *Gene categories file*
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298
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299 This tool can get GO and KEGG categories for some genomes. The three GO categories are GO:MF (Molecular Function - molecular activities of gene products), GO:CC (Cellular Component - where gene products are active), GO:BP (Biological Process - pathways and larger processes made up of the activities of multiple gene products). If your genome is not available, you will also need a file describing the membership of genes in categories. The category file should have two columns with an optional header row. with Gene ID in the first column and category identifier in the second column. As the mapping between categories and genes is usually many-to-many, this table will usually have multiple rows with the same Gene ID and category identifier.
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300
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301 Example:
0
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302
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303 =============== ===========
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304 ENSG00000162526 GO\:0000003
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305 ENSG00000198648 GO\:0000278
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306 ENSG00000112312 GO\:0000278
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307 ENSG00000174442 GO\:0000278
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308 ENSG00000108953 GO\:0000278
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309 =============== ===========
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310
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311 -----
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312
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313 **Outputs**
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314
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315 * This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced.
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316 * Optionally, this tool can also output a plot of the top 10 over-represented GO categories, some diagnostic plots and an RData file, see **Output Options** above.
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317
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318 Example:
0
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319
2
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320 =========== =============== ================ ============ ========== ======================================== ========== =================== ====================
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321 *category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p.adjust.over_rep* *p.adjust.under_rep*
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322 ----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- --------------------
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323 GO\:0005576 0.000054 0.999975 56 142 extracellular region CC 0.394825 1
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324 GO\:0005840 0.000143 0.999988 9 12 ribosome CC 0.394825 1
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325 GO\:0044763 0.000252 0.999858 148 473 single-organism cellular process BP 0.394825 1
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326 GO\:0044699 0.000279 0.999844 158 513 single-organism process BP 0.394825 1
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327 GO\:0065010 0.000428 0.999808 43 108 extracellular membrane-bounded organelle CC 0.394825 1
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328 GO\:0070062 0.000428 0.999808 43 108 extracellular exosome CC 0.394825 1
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329 =========== =============== ================ ============ ========== ======================================== ========== =================== ====================
0
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330
2
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331 -----
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332
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333 **Method options**
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334
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335 3 methods, *Wallenius*, *Sampling* and *Hypergeometric*, can be used to calculate the p-values as follows.
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336
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337 *Wallenius*
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338
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339 approximates the true distribution of numbers of members of a category amongst DE genes by the Wallenius non-central hypergeometric distribution.
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340 This distribution assumes that within a category all genes have the same probability of being chosen. Therefore, this approximation works best when the range in probabilities obtained by the probability weighting function is small. This is the method used by default.
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341
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342 *Sampling*
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343
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344 uses random sampling to approximate the true distribution and uses it to calculate the p-values for over (and under) representation of categories.
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345 Although this is the most accurate method given a high enough value of sampling number, its use quickly becomes computationally prohibitive. It may sometimes be desirable to use random sampling to generate the null distribution for category
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346 membership. For example, to check consistency against results from the Wallenius approximation. This is easily accomplished by using the method option to additionally specify sampling and the number of samples to generate.
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347
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348 *Hypergeometric*
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349
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350 assumes there is no bias in power to detect differential expression at all and calculates the p-values using a standard hypergeometric distribution (no length bias correction is performed). Useful if you wish to test the effect of length bias on your results.
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351 Caution: Hypergeometric should NEVER be used for producing results for biological interpretation of RNA-seq data. If length bias is truly not present in your data, goseq will produce a nearly flat PWF plot, no length bias correction will be applied to your data, and all methods will produce the same results.
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352
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353 -----
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354
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355 **More Information**
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356
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357 In order to account for the length bias inherent to RNA-seq data when performing a GO analysis
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358 (or other category based tests), one cannot simply use the hypergeometric distribution as the null
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359 distribution for category membership, which is appropriate for data without DE length bias, such
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360 as microarray data. GO analysis of RNA-seq data requires the use of random sampling in order
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361 to generate a suitable null distribution for GO category membership and calculate each categories
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362 significance for over representation amongst DE genes.
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363
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364 However, this random sampling is computationally expensive. In most cases, the Wallenius
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365 distribution can be used to approximate the true null distribution, without any significant loss in
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366 accuracy. The goseq package implements this approximation as its default option. The option
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367 to generate the null distribution using random sampling is also included as an option, but users
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368 should be aware that the default number of samples generated will not be enough to accurately
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369 call enrichment when there are a large number of go terms.
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370
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371 Having established a null distribution, each category is then tested for over and under
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372 representation amongst the set of differentially expressed genes and the null is used to calculate a
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373 p-value for under and over representation.
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374
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375 Having performed a GO analysis, you may now wish to interpret the results. If you wish to
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376 identify categories significantly enriched/unenriched below some p-value cutoff, it is necessary to
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377 first apply some kind of multiple hypothesis testing correction. For example, you can identify GO categories over
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378 enriched using a 0.05 FDR (p.adjust) cutoff [Benjamini and Hochberg, 1995].
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379
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380 Unless you are a machine, GO and KEGG category identifiers are probably not very meaningful to you.
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381 Information about each identifier can be obtained from the `Gene Ontology`_ and KEGG_ websites.
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382
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383 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
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384 .. _Gene Ontology: http://www.geneontology.org
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385 .. _KEGG: http://www.genome.jp/kegg
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386
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387 ]]></help>
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388 <citations>
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389 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
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390 </citations>
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391 </tool>