Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 6:9fd8b69e6e68 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 68251c72950b8f31e906cf2c2983952ed3eaec1a
author iuc
date Tue, 26 Feb 2019 10:50:15 -0500
parents 278b189248cd
children 2872c633f07e
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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1 <tool id="dexseq" name="DEXSeq" version="@VERSION@+galaxy1">
0
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2 <description>Determines differential exon usage from count tables</description>
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3 <macros>
2
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4 <import>macros.xml</import>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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5 </macros>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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6 <expand macro="requirements">
4
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7 <requirement type="package" version="1.20.2">r-getopt</requirement>
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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8 <requirement type="package" version="0.2.20">r-rjson</requirement>
2
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9 </expand>
0
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10 <code file="dexseq_helper.py" />
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11 <stdio>
1
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12 <regex match="Execution halted"
4
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13 source="both"
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14 level="fatal"
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15 description="Execution halted." />
1
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16 <regex match="Input-Error 01"
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17 source="both"
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18 level="fatal"
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19 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
0
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20 <regex match="Error in"
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21 source="both"
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22 level="fatal"
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23 description="An undefined error occured, please check your input carefully and contact your administrator." />
0
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24 <regex match="Error:"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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25 source="both"
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26 level="fatal"
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27 description="Error in the R script." />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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28 </stdio>
2
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29 <version_command><![CDATA[
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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30 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: ")")"
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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31 ]]></version_command>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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32 <command><![CDATA[
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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33 mkdir ./html_out &&
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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34 #import json
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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35 Rscript '$__tool_directory__/dexseq.R'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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36 -o '$dexseq_out'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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37 -p \${GALAXY_SLOTS:-4}
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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38 #set $temp_factor_names = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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39 #for $factor in $rep_factorName:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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40 #set $temp_factor = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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41 #set $count_files1 = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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42 #for $file in $factor.countFiles1:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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43 $count_files1.append(str($file))
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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44 #end for
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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45 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
0
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46
2
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47 #set $count_files2 = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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48 #for $file in $factor.countFiles2:
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49 $count_files2.append(str($file))
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50 #end for
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51 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
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52 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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53 #end for
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54 -f '#echo json.dumps(temp_factor_names)#'
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55 -a $gtf
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56 -c $fdr_cutoff
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57 -d $rds
0
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58
2
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59 #if $report:
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60 -r ./html_out
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61 &&
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62 mkdir '$htmlreport.extra_files_path'
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63 &&
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64 cp ./html_out/testForDEU.html $htmlreport
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65 &&
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66 cp -r ./html_out/* '$htmlreport.extra_files_path'
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67 #end if
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68 ]]></command>
0
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69 <inputs>
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70 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
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71 <repeat name="rep_factorName" title="Factor" min="1">
1
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72 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
0
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73 help="Only letters, numbers and underscores will be retained in this field">
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74 <sanitizer>
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75 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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76 </sanitizer>
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77 </param>
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78 <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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79 help="Only letters, numbers and underscores will be retained in this field">
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80 <sanitizer>
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81 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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82 </sanitizer>
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83 </param>
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84 <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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85
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86 <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
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87 help="Only letters, numbers and underscores will be retained in this field">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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88 <sanitizer>
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89 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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90 </sanitizer>
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91 </param>
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92 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
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93 </repeat>
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94 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
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95 label="Visualise the analysis results?"
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96 help="Output an additional HTML file." />
5
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97 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false"
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98 label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" />
0
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99 <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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100 </inputs>
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101 <outputs>
4
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102 <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" />
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103 <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}">
0
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104 <filter>report is True</filter>
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105 </data>
5
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106 <data name="rds_out" format="rdata" from_work_dir="DEXSeqResults.rds" label="DEXSeq rds file on ${on_string}">
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107 <filter>rds is True</filter>
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108 </data>
0
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109 </outputs>
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110 <tests>
2
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111 <!-- Ensure default output works-->
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112 <test expect_num_outputs="1">
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113 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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114 <repeat name="rep_factorName">
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115 <param name="factorName" value="condition"/>
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116 <param name="factorLevel1" value="knockdown"/>
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117 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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118 <param name="factorLevel2" value="control"/>
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119 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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120 </repeat>
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121 <param name="report" value="False"/>
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122 <param name="fdr_cutoff" value="1"/>
4
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123 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
2
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124 </test>
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125 <!-- Ensure report works-->
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126 <test expect_num_outputs="2">
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127 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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128 <repeat name="rep_factorName">
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129 <param name="factorName" value="Treatment"/>
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130 <param name="factorLevel1" value="knockdown"/>
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131 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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132 <param name="factorLevel2" value="control"/>
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133 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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134 </repeat>
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135 <param name="report" value="True"/>
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136 <param name="fdr_cutoff" value="1"/>
4
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137 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
2
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138 </test>
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139 <!-- Ensure two factors works-->
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140 <test expect_num_outputs="1">
0
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141 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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142 <repeat name="rep_factorName">
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143 <param name="factorName" value="condition"/>
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144 <param name="factorLevel1" value="knockdown"/>
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145 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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146 <param name="factorLevel2" value="control"/>
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147 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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148 </repeat>
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149 <repeat name="rep_factorName">
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150 <param name="factorName" value="libtype"/>
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151 <param name="factorLevel1" value="singleend"/>
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152 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
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153 <param name="factorLevel2" value="pairedend"/>
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154 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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155 </repeat>
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156 <param name="report" value="False"/>
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157 <param name="fdr_cutoff" value="0.05"/>
4
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158 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/>
0
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159 </test>
5
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160 <!-- Ensure rds output works-->
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161 <test expect_num_outputs="2">
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162 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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163 <repeat name="rep_factorName">
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164 <param name="factorName" value="condition"/>
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165 <param name="factorLevel1" value="knockdown"/>
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166 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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167 <param name="factorLevel2" value="control"/>
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168 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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169 </repeat>
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170 <param name="report" value="False"/>
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171 <param name="rds" value="True"/>
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172 <param name="fdr_cutoff" value="0.05"/>
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173 <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/>
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174 <output name="rds_out" ftype="rdata" file="dexseq.rds" compare="sim_size"/>
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175 </test>
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176 </tests>
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177 <help><![CDATA[
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178 .. class:: infomark
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179
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180 **What it does**
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181
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182 Inference of differential exon usage in RNA-Seq.
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183
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184
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185 **Inputs**
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186
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187 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
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188 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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189 factor that affects gene expressions. You can also input several secondary factors that might
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190 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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191 You need to select an appropriate count table from your history for each factor level.
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192
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193 The following table gives some examples of factors and their levels:
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194
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195 ========= ============== ===============
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196 Factor Factor level 1 Factor level 2
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197 --------- -------------- ---------------
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198 condition Knockdown Wildtype
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199 --------- -------------- ---------------
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200 treatment Treated Untreated
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201 --------- -------------- ---------------
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202 timePoint Day4 Day1
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203 --------- -------------- ---------------
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204 SeqType SingleEnd PairedEnd
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205 --------- -------------- ---------------
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206 Gender Female Male
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207 ========= ============== ===============
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208
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209 *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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210
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211 **Output**
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212
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213 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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214
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215 ====== ==========================================================
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216 Column Description
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217 ------ ----------------------------------------------------------
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218 1 Gene and exon Identifiers
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219 2 group/gene identifier
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220 3 feature/exon identifier
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221 4 mean of the counts across samples in each feature/exon
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222 5 exon dispersion estimate
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223 6 LRT statistic
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224 7 LRT p-value
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225 8 BH adjusted p-values
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226 9 exon usage coefficient factorLevel 2
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227 10 exon usage coefficient factorLevel 1
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228 11 relative exon usage fold changes
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229 12 GRanges object of the coordinates of the exon/feature
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230 13 matrix of integer counts, of each column containing a sample
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231 14 list of transcripts overlapping with the exon
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232 ====== ==========================================================
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233
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234
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235 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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236 ]]></help>
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237 <citations>
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238 <citation type="doi">10.1101/gr.133744.111</citation>
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239 </citations>
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240 </tool>