Mercurial > repos > iuc > goseq

annotate goseq.xml @ 11:449393187583 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
author iuc
date Wed, 11 Jan 2023 10:13:02 +0000
parents 58aeb8b008c7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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1 <tool id="goseq" name="goseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
0
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2 <description>tests for overrepresented gene categories</description>
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449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.50.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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6 </macros>
8
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7 <edam_topics>
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8 <edam_topic>topic_3308</edam_topic>
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_2436</edam_operation>
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12 </edam_operations>
11
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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13 <xrefs>
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14 <xref type="bio.tools">goseq</xref>
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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15 </xrefs>
0
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">bioconductor-goseq</requirement>
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18 <requirement type="package" version="3.16.0">bioconductor-org.hs.eg.db</requirement>
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19 <requirement type="package" version="3.16.0">bioconductor-org.dm.eg.db</requirement>
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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20 <requirement type="package" version="3.16.0">bioconductor-org.dr.eg.db</requirement>
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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21 <requirement type="package" version="3.16.0">bioconductor-org.mm.eg.db</requirement>
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22 <requirement type="package" version="3.16.0">bioconductor-org.rn.eg.db</requirement>
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23 <requirement type="package" version="1.0.10">r-dplyr</requirement>
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24 <requirement type="package" version="3.4.0">r-ggplot2</requirement>
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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25 <requirement type="package" version="1.7.3">r-optparse</requirement>
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
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26 <requirement type="package" version="1.1.1s">openssl</requirement>
0
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27 </requirements>
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28 <stdio>
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29 <regex match="Execution halted"
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30 source="both"
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31 level="fatal"
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32 description="Execution halted." />
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33 <regex match="Error in"
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34 source="both"
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35 level="fatal"
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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36 description="An undefined error occured, please check your input carefully and contact your administrator." />
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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37 <regex match="Fatal error"
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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38 source="both"
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39 level="fatal"
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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40 description="An undefined error occured, please check your input carefully and contact your administrator." />
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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41 </stdio>
2
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42 <version_command><![CDATA[
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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43 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" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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44 ]]></version_command>
0
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45 <command><![CDATA[
2
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46 Rscript '$__tool_directory__/goseq.r'
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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47
7
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48 --dge_file '$dge_file'
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49 --length_file '$length_file'
2
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50
7
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51 #if $categorySource.catSource == 'getgo'
2
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52 --genome $categorySource.genome
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53 --gene_id $categorySource.gene_id
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54 --fetch_cats '$categorySource.fetchcats'
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55 #elif $categorySource.catSource == 'history'
2
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56 --category_file '$categorySource.category_file'
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57 #end if
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58
7
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59 #if $methods.wallenius
2
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60 --wallenius_tab '$wallenius_tab'
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61 #end if
7
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62 #if $methods.hypergeometric
2
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63 --nobias_tab '$nobias_tab'
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64 #end if
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65
7
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66 --repcnt $methods.repcnt
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67 #if $methods.repcnt != 0
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68 --sampling_tab '$sampling_tab'
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69 #end if
2
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70
7
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71 --p_adj_method '$adv.p_adj_method'
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72 --use_genes_without_cat '$adv.use_genes_without_cat'
2
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73
7
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74 #if $out.topgo_plot
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75 --top_plot '$top_plot'
2
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76 #end if
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77
7
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78 #if str($out.make_plots) == 'TRUE'
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79 --make_plots '$out.make_plots'
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80 --length_bias_plot '$length_bias_plot'
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81 #if $methods.repcnt != 0 and $methods.wallenius
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82 --sample_vs_wallenius_plot '$sample_vs_wallenius_plot'
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83 #end if
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84 #end if
2
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85
7
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86 #if $out.cat_genes
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87 --categories_genes_out_fp '$cat_genes_tab'
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88 #end if
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89
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90 #if $out.rdata_out
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91 --rdata '$rdata'
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92 #end if
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93 ]]></command>
0
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94 <inputs>
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95 <!-- Input Files-->
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96 <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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97 <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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98 <conditional name="categorySource">
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99 <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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100 <option value="getgo" selected="true">Get categories</option>
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101 <option value="history">Use a category file from history</option>
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102 </param>
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103 <when value="getgo">
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104 <param name="genome" type="select" label="Select a genome to use">
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105 <option value="hg38">Human (hg38)</option>
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106 <option value="mm10">Mouse (mm10)</option>
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107 <option value="dm6">Fruit fly (dm6)</option>
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108 <option value="danRer10">Zebrafish (danRer10)</option>
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109 <option value="rn6">Rat (rn6)</option>
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110 </param>
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111 <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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112 <option value="ensGene">Ensembl Gene ID</option>
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113 <option value="knownGene">Entrez Gene ID</option>
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114 <option value="geneSymbol">Gene Symbol</option>
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115 </param>
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116 <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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117 <option value="GO:CC" selected="True">GO: Cellular Component</option>
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118 <option value="GO:BP" selected="True">GO: Biological Process</option>
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119 <option value="GO:MF" selected="True">GO: Molecular Function</option>
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120 <option value="KEGG">KEGG</option>
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121 </param>
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122 </when>
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123 <when value="history">
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124 <param name="category_file" type="data" format="tabular" label="Gene category file"/>
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125 </when>
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126 </conditional>
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127 <!-- Method Options -->
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128 <section name="methods" title="Method Options">
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129 <param name="wallenius" type="boolean" checked="true" label="Use Wallenius method" help="See help for details" />
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130 <param name="hypergeometric" type="boolean" checked="false" label="Use Hypergeometric method" help="Does not use gene length information. See help for details" />
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131 <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" />
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132 </section>
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133 <!-- Advanced Options -->
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134 <section name="adv" title="Advanced Options">
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135 <param name="p_adj_method" type="select" label="Select a method for multiple hypothesis testing correction">
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136 <option value="BH" selected="True">Benjamini-Hochberg [FDR] (1995)</option>
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137 <option value="holm">Holm (1979)</option>
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138 <option value="hommel">Hommel (1988)</option>
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139 <option value="hochberg">Hochberg (1988)</option>
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140 <option value="bonferroni">Bonferroni</option>
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141 <option value="BY">Benjamini - Yekutieli (2001)</option>
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142 </param>
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143 <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"/>
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144 </section>
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145 <!-- Output Options -->
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146 <section name="out" title="Output Options">
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147 <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" />
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148 <param name="make_plots" type="boolean" checked="false" truevalue="TRUE" falsevalue="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" />
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149 <param name="cat_genes" type="boolean" checked="false" label="Extract the DE genes for the categories (GO/KEGG terms)?" help="" />
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150 <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" />
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151 </section>
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152 </inputs>
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153 <outputs>
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154 <data name="wallenius_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Wallenius method">
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155 <filter>methods['wallenius']</filter>
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156 </data>
2
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157 <data name="sampling_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Sampling method">
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158 <filter>methods['repcnt'] != 0</filter>
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159 </data>
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160 <data name="nobias_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Hypergeometric method">
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161 <filter>methods['hypergeometric']</filter>
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162 </data>
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163 <data name="length_bias_plot" format="pdf" label="${tool.name} on ${on_string}: Length bias plot">
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164 <filter>out['make_plots']</filter>
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165 </data>
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166 <data name="sample_vs_wallenius_plot" format="pdf" label="${tool.name} on ${on_string}: Sampling vs Wallenius P-values plot">
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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167 <filter>methods['repcnt'] != 0</filter>
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168 <filter>methods['wallenius']</filter>
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169 <filter>out['make_plots']</filter>
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170 </data>
7
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171 <data name="top_plot" format="pdf" label="${tool.name} on ${on_string}: Top over-represented GO terms plot">
2
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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172 <filter>methods['wallenius']</filter>
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173 <filter>out['topgo_plot']</filter>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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174 </data>
7
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175 <data name="cat_genes_tab" format="tabular" label="${tool.name} on ${on_string}: DE genes for categories (GO/KEGG terms)">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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176 <filter>out['cat_genes']</filter>
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177 </data>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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178 <data name="rdata" format="rdata" label="${tool.name} on ${on_string}: RData file">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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179 <filter>out['rdata_out']</filter>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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180 </data>
0
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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181 </outputs>
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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182 <tests>
7
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183 <!-- Ensure top plot is output and check Wallenius -->
2
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184 <test expect_num_outputs="2">
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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185 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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186 <param name="length_file" value="gene_length.tab" ftype="tabular" />
7
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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187 <conditional name="categorySource">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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188 <param name="catSource" value="history" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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189 <param name="category_file" value="category.tab" ftype="tabular" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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190 </conditional>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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191 <section name="methods">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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192 <param name="wallenius" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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193 <param name="hypergeometric" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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194 <param name="repcnt" value="0"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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195 </section>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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196 <section name="adv">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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197 <param name="p_adj_method" value="BH"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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198 <param name="use_genes_without_cat" value="true" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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199 </section>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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200 <section name="out">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
201 <param name="topgo_plot" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
202 <param name="make_plots" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
203 <param name="cat_genes" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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204 <param name="rdata_out" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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205 </section>
2
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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206 <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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207 <output name="wallenius_tab">
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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208 <assert_contents>
8
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209 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
2
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
210 <has_text_matching expression="GO:0000278.*0.01" />
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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211 </assert_contents>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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diff changeset
212 </output>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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213 </test>
7
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
214 <!-- Ensure getting GO categories works & also DE genes for GO terms-->
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
215 <test expect_num_outputs="2">
0
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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216 <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
084d77515343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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217 <param name="length_file" value="gene_length.tab" ftype="tabular"/>
7
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
218 <conditional name="categorySource">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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219 <param name="catSource" value="getgo" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
220 <param name="genome" value="hg38" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
221 <param name="gene_id" value="ensGene" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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222 <param name="fetchcats" value="GO:CC,GO:BP,GO:MF"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
223 </conditional>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
224 <section name="methods">
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diff changeset
225 <param name="wallenius" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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parents: 6
diff changeset
226 <param name="hypergeometric" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
227 <param name="repcnt" value="0"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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228 </section>
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229 <section name="adv">
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diff changeset
230 <param name="p_adj_method" value="BH"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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231 <param name="use_genes_without_cat" value="true" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
232 </section>
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233 <section name="out">
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parents: 6
diff changeset
234 <param name="topgo_plot" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
235 <param name="make_plots" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
236 <param name="cat_genes" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
237 <param name="rdata_out" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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diff changeset
238 </section>
2
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parents: 1
diff changeset
239 <output name="wallenius_tab">
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
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240 <assert_contents>
8
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parents: 7
diff changeset
241 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
11
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
iuc
parents: 10
diff changeset
242 <has_text_matching expression="GO:0012501.*0.01"/>
7
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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243 </assert_contents>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
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244 </output>
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245 <output name="cat_genes_tab">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
246 <assert_contents>
8
7c9731142105 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e230a8db9e090c6e0ea9577863ec6153df79e145"
iuc
parents: 7
diff changeset
247 <has_text_matching expression="category.*de_genes" />
7
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
248 <has_text_matching expression="GO:0005615.*ENSG00000090402,ENSG00000108953,ENSG00000070961" />
2
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
249 </assert_contents>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
250 </output>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
251 </test>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
252 <!-- Ensure getting GO categories for another genome (zebrafish) works -->
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
253 <test expect_num_outputs="1">
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
254 <param name="dge_file" value="dge_list_zf.tab" ftype="tabular"/>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
255 <param name="length_file" value="gene_length_zf.tab" ftype="tabular"/>
7
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
256 <conditional name="categorySource">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
257 <param name="catSource" value="getgo" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
258 <param name="genome" value="danRer10"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
259 <param name="gene_id" value="ensGene" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
260 <param name="fetchcats" value="GO:CC,GO:BP,GO:MF"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
261 </conditional>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
262 <section name="methods">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
263 <param name="wallenius" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
264 <param name="hypergeometric" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
265 <param name="repcnt" value="0"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
266 </section>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
267 <section name="adv">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
268 <param name="p_adj_method" value="BH"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
269 <param name="use_genes_without_cat" value="true" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
270 </section>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
271 <section name="out">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
272 <param name="topgo_plot" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
273 <param name="make_plots" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
274 <param name="cat_genes" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
275 <param name="rdata_out" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
276 </section>
2
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
277 <output name="wallenius_tab">
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
278 <assert_contents>
8
7c9731142105 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e230a8db9e090c6e0ea9577863ec6153df79e145"
iuc
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diff changeset
279 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
11
449393187583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
iuc
parents: 10
diff changeset
280 <has_text_matching expression="GO:0015748.*0.02" />
2
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
281 </assert_contents>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
282 </output>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
283 </test>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
284 <!-- Ensure length bias plot works -->
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
285 <test expect_num_outputs="2">
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
286 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
287 <param name="length_file" value="gene_length.tab" ftype="tabular" />
7
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
288 <conditional name="categorySource">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
289 <param name="catSource" value="history" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
290 <param name="category_file" value="category.tab" ftype="tabular" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
291 </conditional>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
292 <section name="methods">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
293 <param name="wallenius" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
294 <param name="hypergeometric" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
295 <param name="repcnt" value="0"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
296 </section>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
297 <section name="adv">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
298 <param name="p_adj_method" value="BH"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
299 <param name="use_genes_without_cat" value="true" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
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diff changeset
300 </section>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
301 <section name="out">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
302 <param name="topgo_plot" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
303 <param name="make_plots" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
304 <param name="cat_genes" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
305 <param name="rdata_out" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
306 </section>
2
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
307 <param name="make_plots" value="true" />
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
308 <output name="length_bias_plot" ftype="pdf" file="length_bias_plot.pdf" compare="sim_size" />
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
309 </test>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
310 <!-- Ensure hypergeometric works -->
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
311 <test expect_num_outputs="2">
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
312 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
313 <param name="length_file" value="gene_length.tab" ftype="tabular" />
7
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
314 <conditional name="categorySource">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
315 <param name="catSource" value="history" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
316 <param name="category_file" value="category.tab" ftype="tabular" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
317 </conditional>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
318 <section name="methods">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
319 <param name="wallenius" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
320 <param name="hypergeometric" value="true"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
321 <param name="repcnt" value="0"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
322 </section>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
323 <section name="adv">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
324 <param name="p_adj_method" value="BH"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
325 <param name="use_genes_without_cat" value="true" />
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
326 </section>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
327 <section name="out">
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
328 <param name="topgo_plot" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
329 <param name="make_plots" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
330 <param name="cat_genes" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
331 <param name="rdata_out" value="false"/>
53eff3348302 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e19f8bcaea6f607a1eaa14bb88f2d625ed63df0"
iuc
parents: 6
diff changeset
332 </section>
2
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
333 <output name="nobias_tab" file="nobias.tab" compare="contains" />
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
334 </test>
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
diff changeset
335 <!-- Ensure sampling vs wallenius works -->
25e1e7b40e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
iuc
parents: 1
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336 <test expect_num_outputs="4">
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337 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
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338 <param name="length_file" value="gene_length.tab" ftype="tabular" />
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339 <conditional name="categorySource">
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340 <param name="catSource" value="history" />
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341 <param name="category_file" value="category.tab" ftype="tabular" />
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342 </conditional>
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343 <section name="methods">
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344 <param name="wallenius" value="true"/>
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345 <param name="hypergeometric" value="false"/>
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346 <param name="repcnt" value="1000"/>
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347 </section>
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348 <section name="adv">
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349 <param name="p_adj_method" value="BH"/>
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350 <param name="use_genes_without_cat" value="true" />
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351 </section>
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352 <section name="out">
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353 <param name="topgo_plot" value="false"/>
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354 <param name="make_plots" value="true"/>
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355 <param name="cat_genes" value="false"/>
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356 <param name="rdata_out" value="false"/>
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357 </section>
2
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358 <output name="sampling_tab" file="samp.tab" compare="sim_size" />
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359 <output name="length_bias_plot" ftype="pdf" file="length_bias_plot.pdf" compare="sim_size" />
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360 <output name="sample_vs_wallenius_plot" ftype="pdf" file="sample_vs_wallenius_plot.pdf" compare="sim_size" />
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361 </test>
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362 <!-- Ensure RData output works -->
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363 <test expect_num_outputs="2">
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364 <param name="dge_file" value="dge_list.tab" ftype="tabular" />
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365 <param name="length_file" value="gene_length.tab" ftype="tabular" />
7
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366 <conditional name="categorySource">
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367 <param name="catSource" value="history" />
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368 <param name="category_file" value="category.tab" ftype="tabular" />
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369 </conditional>
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370 <section name="methods">
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371 <param name="wallenius" value="true"/>
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372 <param name="hypergeometric" value="false"/>
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373 <param name="repcnt" value="0"/>
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374 </section>
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375 <section name="adv">
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376 <param name="p_adj_method" value="BH"/>
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377 <param name="use_genes_without_cat" value="true" />
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378 </section>
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379 <section name="out">
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380 <param name="topgo_plot" value="false"/>
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381 <param name="make_plots" value="false"/>
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382 <param name="cat_genes" value="false"/>
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383 <param name="rdata_out" value="true"/>
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384 </section>
2
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385 <output name="rdata" file="goseq_analysis.RData" compare="sim_size" />
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386 </test>
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387 </tests>
2
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388 <help><![CDATA[
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389
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390 .. class:: infomark
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391
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392 **What it does**
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393
2
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394 `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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395
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396 Options map closely to the excellent goseq manual_.
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397
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398 -----
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399
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400 **Inputs**
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401
2
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402 *Differentially expressed genes file*
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403
11
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404 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 on rows" tool to create a True / False column for your dataset.
2
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405
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406 Example:
0
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407
2
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408 =============== =====
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409 ENSG00000236824 False
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410 ENSG00000162526 False
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411 ENSG00000090402 True
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412 ENSG00000169188 False
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413 ENSG00000124103 False
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414 =============== =====
0
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415
2
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416 *Gene lengths file*
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417
2
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418 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.
0
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419
2
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420 Example:
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421
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422 =============== =====
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423 ENSG00000236824 13458
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424 ENSG00000162526 2191
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425 ENSG00000090402 6138
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426 ENSG00000169188 3245
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427 ENSG00000124103 1137
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428 =============== =====
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429
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430 *Gene categories file*
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431
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432 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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433
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434 Example:
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435
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436 =============== ===========
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437 ENSG00000162526 GO\:0000003
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438 ENSG00000198648 GO\:0000278
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439 ENSG00000112312 GO\:0000278
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440 ENSG00000174442 GO\:0000278
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441 ENSG00000108953 GO\:0000278
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442 =============== ===========
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443
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444 -----
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445
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446 **Outputs**
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447
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448 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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449
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450 Example:
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451
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452 =========== =============== ================ ============ ========== ======================================== ========== =================== ====================
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453 *category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p_adjust_over_rep* *p_adjust_under_rep*
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454 ----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- --------------------
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455 GO\:0005576 0.000054 0.999975 56 142 extracellular region CC 0.394825 1
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456 GO\:0005840 0.000143 0.999988 9 12 ribosome CC 0.394825 1
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457 GO\:0044763 0.000252 0.999858 148 473 single-organism cellular process BP 0.394825 1
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458 GO\:0044699 0.000279 0.999844 158 513 single-organism process BP 0.394825 1
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459 GO\:0065010 0.000428 0.999808 43 108 extracellular membrane-bounded organelle CC 0.394825 1
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460 GO\:0070062 0.000428 0.999808 43 108 extracellular exosome CC 0.394825 1
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461 =========== =============== ================ ============ ========== ======================================== ========== =================== ====================
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462
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463 Optionally, this tool can also output:
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464 * a plot of the top 10 over-represented GO categories
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465 * some diagnostic plots
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466 * a tabular with the differentially expressed genes in categories (GO/KEGG terms)
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467 * an RData file
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468
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469 -----
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470
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471 **Method options**
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472
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473 3 methods, *Wallenius*, *Sampling* and *Hypergeometric*, can be used to calculate the p-values as follows.
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474
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475 *Wallenius*
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476
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477 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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478 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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479
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480 *Sampling*
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481
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482 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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483 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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484 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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485
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486 *Hypergeometric*
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487
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488 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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489 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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490
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491 -----
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492
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493 **More Information**
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494
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495 In order to account for the length bias inherent to RNA-seq data when performing a GO analysis
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496 (or other category based tests), one cannot simply use the hypergeometric distribution as the null
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497 distribution for category membership, which is appropriate for data without DE length bias, such
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498 as microarray data. GO analysis of RNA-seq data requires the use of random sampling in order
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499 to generate a suitable null distribution for GO category membership and calculate each categories
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500 significance for over representation amongst DE genes.
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501
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502 However, this random sampling is computationally expensive. In most cases, the Wallenius
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503 distribution can be used to approximate the true null distribution, without any significant loss in
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504 accuracy. The goseq package implements this approximation as its default option. The option
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505 to generate the null distribution using random sampling is also included as an option, but users
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506 should be aware that the default number of samples generated will not be enough to accurately
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507 call enrichment when there are a large number of go terms.
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508
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509 Having established a null distribution, each category is then tested for over and under
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510 representation amongst the set of differentially expressed genes and the null is used to calculate a
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511 p-value for under and over representation.
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512
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513 Having performed a GO analysis, you may now wish to interpret the results. If you wish to
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514 identify categories significantly enriched/unenriched below some p-value cutoff, it is necessary to
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515 first apply some kind of multiple hypothesis testing correction. For example, you can identify GO categories over
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516 enriched using a 0.05 FDR (p.adjust) cutoff [Benjamini and Hochberg, 1995].
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517
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518 Unless you are a machine, GO and KEGG category identifiers are probably not very meaningful to you.
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519 Information about each identifier can be obtained from the `Gene Ontology`_ and KEGG_ websites.
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520
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521 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
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522 .. _Gene Ontology: http://www.geneontology.org
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523 .. _KEGG: http://www.genome.jp/kegg
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524
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525 ]]></help>
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526 <citations>
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527 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
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528 </citations>
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11385d227014 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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529 </tool>