Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 1:36fe30ece23b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e2ab82632ee80aa2347545b2f21235d851b8c36a-dirty
author iuc
date Fri, 25 Sep 2015 14:05:00 -0400
parents 276833129f97
children b19cb9385f28
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276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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1 <tool id="dexseq" name="DEXSeq" version="1.0">
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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2 <description>Determines differential exon usage from count tables</description>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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3 <requirements>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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4 <requirement type="package" version="1.14.2">dexseq</requirement>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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5 </requirements>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
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6 <code file="dexseq_helper.py" />
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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7 <command>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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8 <![CDATA[
1
36fe30ece23b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e2ab82632ee80aa2347545b2f21235d851b8c36a-dirty
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9 mkdir ./html_out &&
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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10 #import json
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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11 Rscript $__tool_directory__/dexseq.R
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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12 -o "$dexseq_out"
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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13 -p 6
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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14 #set $temp_factor_names = list()
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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15 #for $factor in $rep_factorName:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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16 #set $temp_factor = list()
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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17 #for $level in $factor.rep_factorLevel:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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18 #set $count_files = list()
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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19 #for $file in $level.countsFile:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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20 $count_files.append(str($file))
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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21 #end for
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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22 $temp_factor.append( {str($level.factorLevel): $count_files} )
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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23 #end for
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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24 $temp_factor_names.append([str($factor.factorName), $temp_factor])
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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25 #end for
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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26 -f '#echo json.dumps(temp_factor_names)#'
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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27 -a $gtf
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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28 #if $report:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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29 -r ./html_out
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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30 #end if
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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31 -c $fdr_cutoff
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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32 &&
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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33 mkdir $htmlreport.extra_files_path
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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34 &&
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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35 cp ./html_out/testForDEU.html $htmlreport
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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36 &&
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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37 cp -r ./html_out/* $htmlreport.extra_files_path
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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38 &&
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39 ]]>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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40 </command>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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41 <stdio>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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42 <regex match="Execution halted"
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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43 source="both"
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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44 level="fatal"
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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45 description="Execution halted." />
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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46 <regex match="Input-Error 01"
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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47 source="both"
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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48 level="fatal"
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49 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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50 <regex match="Error in"
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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51 source="both"
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52 level="fatal"
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53 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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54 </stdio>
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55 <inputs>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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56 <param name="gtf" type="data" label="GTF file created from DEXSeq-Count tool"/>
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57 <repeat name="rep_factorName" title="Factor" min="1">
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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58 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
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59 help="Only letters, numbers and underscores will be retained in this field">
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60 <sanitizer>
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61 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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62 </sanitizer>
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63 </param>
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64 <repeat name="rep_factorLevel" title="Factor level" min="2" max="2" default="2">
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65 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level"
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66 help="Only letters, numbers and underscores will be retained in this field">
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67 <sanitizer>
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68 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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69 </sanitizer>
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70 </param>
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71 <param name="countsFile" type="data" multiple="true" label="Counts file"/>
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72 </repeat>
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73 </repeat>
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74 <param name="report" type="boolean" truevalue="" falsevalue="" checked="true"
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75 label="Visualise the analysis results?"
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76 help="output an additional html file" />
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77 <param name="fdr_cutoff" type="float" min="0" max="1" value="0.05" label="All the genes under this FDR threshold will be shown in the html report."/>
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78 </inputs>
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79
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80 <outputs>
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81 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/>
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82 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
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83 <filter>report == True</filter>
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84 </data>
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85 </outputs>
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86
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87 <code file="dexseq_helper.py" />
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88 <tests>
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89 <test>
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90 <param name="gtf" value="dexseq.gtf" ftype="bed"/>
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91 <repeat name="rep_factorName">
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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92 <param name="factorName" value="condition" ftype="bed"/>
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93 <repeat name="rep_factorLevel">
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94 <param name="factorLevel" type="text" value="knockdown"/>
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95 <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
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96 </repeat>
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97 <repeat name="rep_factorLevel">
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98 <param name="factorLevel" type="text" value="knockdown"/>
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99 <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
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100 </repeat>
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101 <repeat name="rep_factorLevel">
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102 <param name="factorLevel" type="text" value="knockdown"/>
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103 <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
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104 </repeat>
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105 <repeat name="rep_factorLevel">
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106 <param name="factorLevel" type="text" value="control"/>
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107 <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
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108 </repeat>
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109 <repeat name="rep_factorLevel">
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110 <param name="factorLevel" type="text" value="control"/>
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111 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
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112 </repeat>
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113 <repeat name="rep_factorLevel">
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114 <param name="factorLevel" type="text" value="control"/>
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115 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
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116 </repeat>
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117 <repeat name="rep_factorLevel">
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118 <param name="factorLevel" type="text" value="control"/>
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119 <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
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120 </repeat>
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121 </repeat>
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122 <repeat name="rep_factorName">
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123 <param name="factorName" value="libtype" ftype="bed"/>
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124 <repeat name="rep_factorLevel">
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125 <param name="factorLevel" type="text" value="singleend"/>
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126 <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
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127 </repeat>
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128 <repeat name="rep_factorLevel">
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129 <param name="factorLevel" type="text" value="singleend"/>
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130 <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
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131 </repeat>
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132 <repeat name="rep_factorLevel">
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133 <param name="factorLevel" type="text" value="singleend"/>
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134 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
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135 </repeat>
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136 <repeat name="rep_factorLevel">
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137 <param name="factorLevel" type="text" value="pairedend"/>
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138 <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
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139 </repeat>
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140 <repeat name="rep_factorLevel">
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141 <param name="factorLevel" type="text" value="pairedend"/>
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142 <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
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143 </repeat>
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144 <repeat name="rep_factorLevel">
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145 <param name="factorLevel" type="text" value="pairedend"/>
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146 <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
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147 </repeat>
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148 <repeat name="rep_factorLevel">
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149 <param name="factorLevel" type="text" value="pairedend"/>
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150 <param name="countsFile" ftype="tabular" value="untreated4fb.txt"/>
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151 </repeat>
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152 </repeat>
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153 <param name="report" type="boolean" value="False"/>
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154 <param name="fdr_cutoff" value="0.05"/>
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155 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
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156 </test>
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157 </tests>
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158 <help>
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159 <![CDATA[
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160 .. class:: infomark
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161
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162 **What it does**
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163
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164 Inference of differential exon usage in RNA-Seq.
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165
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166
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167 **Inputs**
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168
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169 DEXSeq_ takes count tables that generated from the dexseq_count as input. Count tables must be generated for each sample individually.
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170 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary
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171 factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might
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172 influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states.
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173 You need to select appropriate count table from your history for each factor level.
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174
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175 The following table gives some examples of factors and their levels:
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176
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177 ========= ============== ===============
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178 Factor Factor level 1 Factor level 2
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179 --------- -------------- ---------------
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180 condition Knockdown Wildtype
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181 --------- -------------- ---------------
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182 treatment Treated Untreated
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183 --------- -------------- ---------------
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184 timePoint Day4 Day1
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185 --------- -------------- ---------------
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186 SeqType SingleEnd PairedEnd
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187 --------- -------------- ---------------
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188 Gender Female Male
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189 ========= ============== ===============
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190
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191 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'condition' given in 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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192
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193 **Output**
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194
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195 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
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196
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197 ====== ==========================================================
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198 Column Description
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199 ------ ----------------------------------------------------------
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200 1 Gene and exon Identifiers
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201 2 group/gene identifier
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202 3 feature/exon identifier
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203 4 mean of the counts across samples in each feature/exon
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204 5 exon dispersion estimate
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205 6 LRT statistic
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206 7 LRT p-value
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207 8 BH adjusted p-values
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208 9 exon usage coefficient factorLevel 2
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209 10 exon usage coefficient factorLevel 1
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210 11 relative exon usage fold changes
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211 12 GRanges object of the coordinates of the exon/feature
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212 13 matrix of integer counts, of each column containing a sample
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213 14 list of transcripts overlapping with the exon
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214 ====== ==========================================================
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215
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216
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217 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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218 ]]>
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219 </help>
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220 <citations>
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221 <citation type="doi">10.1101/gr.133744.111</citation>
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222 </citations>
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223 </tool>