Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 18:ffa256d657b2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
author iuc
date Fri, 31 Jan 2025 18:00:29 +0000
parents d104044e4257
children
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1 <tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>Determines differential exon usage from count tables</description>
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3 <macros>
8
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
0
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8 <code file="dexseq_helper.py" />
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9 <stdio>
7
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10 <regex match="Execution halted"
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11 source="both"
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12 level="fatal"
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13 description="Execution halted." />
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14 <regex match="Input-Error 01"
10
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15 source="both"
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16 level="fatal"
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17 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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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="Error:"
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23 source="both"
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24 level="fatal"
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25 description="Error in the R script." />
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26 </stdio>
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27 <version_command><![CDATA[
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28 echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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29 ]]></version_command>
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30 <command><![CDATA[
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31 mkdir ./html_out &&
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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32 #import json
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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33 Rscript '$__tool_directory__/dexseq.R'
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34 -o '$dexseq_out'
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35 -p \${GALAXY_SLOTS:-4}
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36 #set $temp_factor_names = list()
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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37 #for $factor in $rep_factorName:
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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38 #set $temp_factor = list()
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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39 #set $count_files1 = list()
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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40 #for $file in $factor.countFiles1:
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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41 $count_files1.append(str($file))
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42 #end for
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43 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
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44
8
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45 #set $count_files2 = list()
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46 #for $file in $factor.countFiles2:
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47 $count_files2.append(str($file))
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48 #end for
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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49 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
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50 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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51 #end for
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52 -f '#echo json.dumps(temp_factor_names)#'
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53 -a $gtf
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54 -c $fdr_cutoff
11
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55 -d $rds
4
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56
8
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57 #if $report:
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58 -r ./html_out
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59 &&
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60 mkdir '$htmlreport.extra_files_path'
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61 &&
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62 cp ./html_out/testForDEU.html $htmlreport
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63 &&
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64 cp -r ./html_out/* '$htmlreport.extra_files_path'
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65 #end if
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66 ]]></command>
0
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67 <inputs>
3
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68 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
0
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69 <repeat name="rep_factorName" title="Factor" min="1">
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70 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
0
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71 help="Only letters, numbers and underscores will be retained in this field">
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72 <sanitizer>
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73 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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74 </sanitizer>
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75 </param>
5
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76 <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
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77 help="Only letters, numbers and underscores will be retained in this field">
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78 <sanitizer>
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79 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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80 </sanitizer>
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81 </param>
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82 <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
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83
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84 <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
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85 help="Only letters, numbers and underscores will be retained in this field">
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86 <sanitizer>
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87 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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88 </sanitizer>
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89 </param>
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90 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
0
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91 </repeat>
4
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92 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
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93 label="Visualise the analysis results?"
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94 help="Output an additional HTML file." />
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95 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false"
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96 label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" />
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97 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
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98 </inputs>
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99 <outputs>
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100 <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result">
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101 <actions>
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102 <action name="column_names" type="metadata" default="GeneID,ExonID,Exon base mean,Dispersion,Stat,p-value,p-adj,X1_group1,X2_group2,log2(FC),Chr. name,Start,End,Width,Strand,Raw counts"/>
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103 </actions>
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104 </data>
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105 <data name="htmlreport" format="html" label="${tool.name} on ${on_string}: report">
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106 <filter>report is True</filter>
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107 </data>
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108 <data name="rds_out" format="rds" from_work_dir="DEXSeqResults.rds" label="${tool.name} on ${on_string}: rds file">
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109 <filter>rds is True</filter>
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110 </data>
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111 </outputs>
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112 <tests>
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113 <!-- Ensure default output works-->
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114 <test expect_num_outputs="1">
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115 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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116 <repeat name="rep_factorName">
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117 <param name="factorName" value="condition"/>
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118 <param name="factorLevel1" value="knockdown"/>
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119 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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120 <param name="factorLevel2" value="control"/>
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121 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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122 </repeat>
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123 <param name="report" value="False"/>
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124 <param name="fdr_cutoff" value="1"/>
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125 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
8
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126 </test>
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127 <!-- Ensure report works-->
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128 <test expect_num_outputs="2">
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129 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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130 <repeat name="rep_factorName">
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131 <param name="factorName" value="Treatment"/>
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132 <param name="factorLevel1" value="knockdown"/>
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133 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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134 <param name="factorLevel2" value="control"/>
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135 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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136 </repeat>
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137 <param name="report" value="True"/>
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138 <param name="fdr_cutoff" value="1"/>
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139 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
8
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140 </test>
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141 <!-- Ensure two factors works-->
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142 <test expect_num_outputs="1">
5
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143 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
0
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144 <repeat name="rep_factorName">
4
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145 <param name="factorName" value="condition"/>
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146 <param name="factorLevel1" value="knockdown"/>
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147 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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148 <param name="factorLevel2" value="control"/>
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149 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
0
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150 </repeat>
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151 <repeat name="rep_factorName">
4
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152 <param name="factorName" value="libtype"/>
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153 <param name="factorLevel1" value="singleend"/>
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154 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
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155 <param name="factorLevel2" value="pairedend"/>
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156 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
0
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157 </repeat>
4
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158 <param name="report" value="False"/>
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159 <param name="fdr_cutoff" value="0.05"/>
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160 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/>
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161 </test>
11
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162 <!-- Ensure rds output works-->
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163 <test expect_num_outputs="2">
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164 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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165 <repeat name="rep_factorName">
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166 <param name="factorName" value="condition"/>
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167 <param name="factorLevel1" value="knockdown"/>
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168 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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169 <param name="factorLevel2" value="control"/>
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170 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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171 </repeat>
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172 <param name="report" value="False"/>
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173 <param name="rds" value="True"/>
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174 <param name="fdr_cutoff" value="0.05"/>
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175 <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/>
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176 <output name="rds_out" ftype="rds" file="dexseq.rds" compare="sim_size"/>
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177 </test>
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178 </tests>
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179 <help><![CDATA[
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180 .. class:: infomark
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181
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182 **What it does**
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183
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184 Inference of differential exon usage in RNA-Seq.
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185
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187 **Inputs**
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188
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189 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
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190 DEXSeq_ is capable of handling multiple factors that affect your experiment. The first factor you input is considered to be the primary
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191 factor that affects gene expressions. You can also input several secondary factors that might
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192 influence your experiment but the final output will be changes in genes due to primary factor in the presence of secondary factors. Each factor has two levels/states.
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193 You need to select an appropriate count table from your history for each factor level.
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194
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195 The following table gives some examples of factors and their levels:
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196
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197 ========= ============== ===============
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198 Factor Factor level 1 Factor level 2
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199 --------- -------------- ---------------
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200 condition Knockdown Wildtype
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201 --------- -------------- ---------------
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202 treatment Treated Untreated
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203 --------- -------------- ---------------
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204 timePoint Day4 Day1
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205 --------- -------------- ---------------
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206 SeqType SingleEnd PairedEnd
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207 --------- -------------- ---------------
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208 Gender Female Male
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209 ========= ============== ===============
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210
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211 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level 2. Here the order of factor levels is important. For example, for the factor 'condition' given in the above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples.
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213 **Output**
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214
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215 DEXSeq_ generates a tabular file containing the different columns and an optional html report. It can also ouput the DEXSeqResults R object that can be used with the plotDEXSeq tool to visualise individual genes.
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217 ====== ==========================================================
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218 Column Description
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219 ------ ----------------------------------------------------------
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220 1 Gene and exon Identifiers
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221 2 group/gene identifier
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222 3 feature/exon identifier
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223 4 mean of the counts across samples in each feature/exon
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224 5 exon dispersion estimate
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225 6 LRT statistic
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226 7 LRT p-value
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227 8 BH adjusted p-values
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228 9 exon usage coefficient factorLevel 2
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229 10 exon usage coefficient factorLevel 1
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230 11 relative exon usage fold changes
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231 12 GRanges object of the coordinates of the exon/feature
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232 13 matrix of integer counts, of each column containing a sample
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233 14 list of transcripts overlapping with the exon
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234 ====== ==========================================================
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235
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236
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237 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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238 ]]></help>
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239 <citations>
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240 <citation type="doi">10.1101/gr.133744.111</citation>
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241 </citations>
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242 </tool>