Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 4:7069d55968fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
author iuc
date Sun, 27 Sep 2015 14:06:28 -0400
parents a26a82bed63f
children 28a2181df3b9
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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"
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9 source="both"
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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." />
4
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16 <regex match="Error in"
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
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17 source="both"
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18 level="fatal"
3
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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>
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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
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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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:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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32 #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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33 #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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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} )
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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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 -c $fdr_cutoff
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
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43
0
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44 #if $report:
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45 -r ./html_out
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46 &&
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
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47 mkdir $htmlreport.extra_files_path
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48 &&
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
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49 cp ./html_out/testForDEU.html $htmlreport
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
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50 &&
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
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51 cp -r ./html_out/* $htmlreport.extra_files_path
0
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52 #end if
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53
0
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54 ]]>
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55 </command>
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56 <inputs>
3
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57 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
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58 <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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59 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
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60 help="Only letters, numbers and underscores will be retained in this field">
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61 <sanitizer>
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62 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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63 </sanitizer>
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64 </param>
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65 <repeat name="rep_factorLevel" title="Factor level" min="2" max="2" default="2">
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66 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level"
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67 help="Only letters, numbers and underscores will be retained in this field">
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68 <sanitizer>
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69 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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70 </sanitizer>
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71 </param>
3
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72 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/>
0
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73 </repeat>
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74 </repeat>
4
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75 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
0
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76 label="Visualise the analysis results?"
4
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77 help="Output an additional HTML file." />
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78 <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"/>
0
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79 </inputs>
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80 <outputs>
4
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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}">
4
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83 <filter>report is True</filter>
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84 </data>
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85 </outputs>
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86 <tests>
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87 <test>
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88 <param name="gtf" value="dexseq.gtf" ftype="bed"/>
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89 <repeat name="rep_factorName">
4
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90 <param name="factorName" value="condition"/>
0
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91 <repeat name="rep_factorLevel">
4
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92 <param name="factorLevel" value="knockdown"/>
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93 <param name="countsFile" value="treated1fb.txt,treated2fb.txt,treated3fb.txt"/>
0
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94 </repeat>
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95 <repeat name="rep_factorLevel">
4
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96 <param name="factorLevel" value="control"/>
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97 <param name="countsFile" value="untreated1fb.txt,untreated2fb.txt,untreated2fb.txt,untreated3fb.txt"/>
0
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98 </repeat>
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99 </repeat>
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100 <repeat name="rep_factorName">
4
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101 <param name="factorName" value="libtype"/>
0
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102 <repeat name="rep_factorLevel">
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103 <param name="factorLevel" value="singleend"/>
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104 <param name="countsFile" ftype="tabular" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt"/>
0
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105 </repeat>
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106 <repeat name="rep_factorLevel">
4
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107 <param name="factorLevel" value="pairedend"/>
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108 <param name="countsFile" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt"/>
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109 </repeat>
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110 </repeat>
4
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111 <param name="report" value="False"/>
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112 <param name="fdr_cutoff" value="0.05"/>
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113 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
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114 </test>
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115 </tests>
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116 <help>
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117 <![CDATA[
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118 .. class:: infomark
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119
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120 **What it does**
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121
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122 Inference of differential exon usage in RNA-Seq.
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123
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124
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125 **Inputs**
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126
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127 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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128 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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129 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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130 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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131 You need to select appropriate count table from your history for each factor level.
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132
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133 The following table gives some examples of factors and their levels:
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134
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135 ========= ============== ===============
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136 Factor Factor level 1 Factor level 2
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137 --------- -------------- ---------------
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138 condition Knockdown Wildtype
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139 --------- -------------- ---------------
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140 treatment Treated Untreated
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141 --------- -------------- ---------------
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142 timePoint Day4 Day1
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143 --------- -------------- ---------------
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144 SeqType SingleEnd PairedEnd
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145 --------- -------------- ---------------
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146 Gender Female Male
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147 ========= ============== ===============
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148
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149 *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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150
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151 **Output**
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152
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153 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
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154
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155 ====== ==========================================================
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156 Column Description
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157 ------ ----------------------------------------------------------
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158 1 Gene and exon Identifiers
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159 2 group/gene identifier
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160 3 feature/exon identifier
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161 4 mean of the counts across samples in each feature/exon
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162 5 exon dispersion estimate
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163 6 LRT statistic
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164 7 LRT p-value
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165 8 BH adjusted p-values
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166 9 exon usage coefficient factorLevel 2
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167 10 exon usage coefficient factorLevel 1
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168 11 relative exon usage fold changes
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169 12 GRanges object of the coordinates of the exon/feature
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170 13 matrix of integer counts, of each column containing a sample
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171 14 list of transcripts overlapping with the exon
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172 ====== ==========================================================
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173
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174
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175 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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176 ]]>
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177 </help>
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178 <citations>
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179 <citation type="doi">10.1101/gr.133744.111</citation>
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180 </citations>
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181 </tool>