Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 3:a26a82bed63f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
author iuc
date Fri, 25 Sep 2015 16:26:39 -0400
parents b19cb9385f28
children 7069d55968fb
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1 <tool id="dexseq" name="DEXSeq" version="1.0">
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2 <description>Determines differential exon usage from count tables</description>
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3 <requirements>
2
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4 <requirement type="package" version="1.14">dexseq</requirement>
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5 </requirements>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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6 <code file="dexseq_helper.py" />
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7 <stdio>
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8 <regex match="Execution halted"
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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9 source="both"
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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10 level="fatal"
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11 description="Execution halted." />
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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12 <regex match="Input-Error 01"
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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13 source="both"
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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14 level="fatal"
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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15 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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16 <regex match="Error in"
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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17 source="both"
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18 level="fatal"
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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19 description="An undefined error occured, please check your intput carefully and contact your administrator." />
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
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20 </stdio>
0
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21 <command>
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22 <![CDATA[
1
36fe30ece23b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e2ab82632ee80aa2347545b2f21235d851b8c36a-dirty
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23 mkdir ./html_out &&
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24 #import json
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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25 Rscript $__tool_directory__/dexseq.R
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26 -o "$dexseq_out"
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27 -p 6
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28 #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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29 #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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30 #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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31 #for $level in $factor.rep_factorLevel:
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32 #set $count_files = list()
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33 #for $file in $level.countsFile:
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34 $count_files.append(str($file))
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35 #end for
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36 $temp_factor.append( {str($level.factorLevel): $count_files} )
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37 #end for
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38 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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39 #end for
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40 -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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41 -a $gtf
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42 #if $report:
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43 -r ./html_out
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44 #end if
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45 -c $fdr_cutoff
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46 &&
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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47 mkdir $htmlreport.extra_files_path
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48 &&
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49 cp ./html_out/testForDEU.html $htmlreport
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50 &&
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51 cp -r ./html_out/* $htmlreport.extra_files_path
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52 &&
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53 ]]>
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54 </command>
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55 <inputs>
3
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56 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
0
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57 <repeat name="rep_factorName" title="Factor" min="1">
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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>
3
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71 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/>
0
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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 <outputs>
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80 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/>
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81 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
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82 <filter>report == True</filter>
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83 </data>
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="gtf" value="dexseq.gtf" ftype="bed"/>
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88 <repeat name="rep_factorName">
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89 <param name="factorName" value="condition" ftype="bed"/>
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90 <repeat name="rep_factorLevel">
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91 <param name="factorLevel" type="text" value="knockdown"/>
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92 <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
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93 </repeat>
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94 <repeat name="rep_factorLevel">
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95 <param name="factorLevel" type="text" value="knockdown"/>
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96 <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
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97 </repeat>
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98 <repeat name="rep_factorLevel">
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99 <param name="factorLevel" type="text" value="knockdown"/>
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100 <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
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101 </repeat>
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102 <repeat name="rep_factorLevel">
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103 <param name="factorLevel" type="text" value="control"/>
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104 <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
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105 </repeat>
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106 <repeat name="rep_factorLevel">
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107 <param name="factorLevel" type="text" value="control"/>
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108 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
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109 </repeat>
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110 <repeat name="rep_factorLevel">
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111 <param name="factorLevel" type="text" value="control"/>
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112 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
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113 </repeat>
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114 <repeat name="rep_factorLevel">
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115 <param name="factorLevel" type="text" value="control"/>
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116 <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
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117 </repeat>
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118 </repeat>
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119 <repeat name="rep_factorName">
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120 <param name="factorName" value="libtype" ftype="bed"/>
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121 <repeat name="rep_factorLevel">
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122 <param name="factorLevel" type="text" value="singleend"/>
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123 <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
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124 </repeat>
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125 <repeat name="rep_factorLevel">
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126 <param name="factorLevel" type="text" value="singleend"/>
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127 <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
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128 </repeat>
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129 <repeat name="rep_factorLevel">
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130 <param name="factorLevel" type="text" value="singleend"/>
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131 <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
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132 </repeat>
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133 <repeat name="rep_factorLevel">
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134 <param name="factorLevel" type="text" value="pairedend"/>
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135 <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
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136 </repeat>
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137 <repeat name="rep_factorLevel">
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138 <param name="factorLevel" type="text" value="pairedend"/>
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139 <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
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140 </repeat>
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141 <repeat name="rep_factorLevel">
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142 <param name="factorLevel" type="text" value="pairedend"/>
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143 <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
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144 </repeat>
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145 <repeat name="rep_factorLevel">
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146 <param name="factorLevel" type="text" value="pairedend"/>
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147 <param name="countsFile" ftype="tabular" value="untreated4fb.txt"/>
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148 </repeat>
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149 </repeat>
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150 <param name="report" type="boolean" value="False"/>
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151 <param name="fdr_cutoff" value="0.05"/>
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152 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
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153 </test>
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154 </tests>
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155 <help>
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156 <![CDATA[
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157 .. class:: infomark
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158
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159 **What it does**
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160
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161 Inference of differential exon usage in RNA-Seq.
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162
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163
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164 **Inputs**
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165
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166 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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167 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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168 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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169 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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170 You need to select appropriate count table from your history for each factor level.
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171
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172 The following table gives some examples of factors and their levels:
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173
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174 ========= ============== ===============
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175 Factor Factor level 1 Factor level 2
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176 --------- -------------- ---------------
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177 condition Knockdown Wildtype
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178 --------- -------------- ---------------
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179 treatment Treated Untreated
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180 --------- -------------- ---------------
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181 timePoint Day4 Day1
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182 --------- -------------- ---------------
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183 SeqType SingleEnd PairedEnd
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184 --------- -------------- ---------------
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185 Gender Female Male
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186 ========= ============== ===============
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187
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188 *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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189
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190 **Output**
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191
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192 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
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193
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194 ====== ==========================================================
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195 Column Description
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196 ------ ----------------------------------------------------------
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197 1 Gene and exon Identifiers
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198 2 group/gene identifier
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199 3 feature/exon identifier
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200 4 mean of the counts across samples in each feature/exon
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201 5 exon dispersion estimate
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202 6 LRT statistic
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203 7 LRT p-value
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204 8 BH adjusted p-values
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205 9 exon usage coefficient factorLevel 2
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206 10 exon usage coefficient factorLevel 1
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207 11 relative exon usage fold changes
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208 12 GRanges object of the coordinates of the exon/feature
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209 13 matrix of integer counts, of each column containing a sample
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210 14 list of transcripts overlapping with the exon
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211 ====== ==========================================================
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212
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213
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214 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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215 ]]>
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216 </help>
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217 <citations>
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218 <citation type="doi">10.1101/gr.133744.111</citation>
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219 </citations>
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220 </tool>