Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 7:469c0d7489bd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
author iuc
date Sun, 29 Jan 2017 06:59:23 -0500
parents 28a2181df3b9
children 0ccbed58b270
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469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
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1 <tool id="dexseq" name="DEXSeq" version="1.20.1">
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2 <description>Determines differential exon usage from count tables</description>
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3 <requirements>
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4 <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
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6 <requirement type="package" version="0.2.15">r-rjson</requirement>
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7 </requirements>
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8 <code file="dexseq_helper.py" />
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9 <stdio>
7
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10 <regex match="Execution halted"
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11 source="both"
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12 level="fatal"
3
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13 description="Execution halted." />
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14 <regex match="Input-Error 01"
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
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15 source="both"
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16 level="fatal"
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17 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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18 <regex match="Error in"
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19 source="both"
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20 level="fatal"
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21 description="An undefined error occured, please check your input carefully and contact your administrator." />
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22 <regex match="Error:"
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23 source="both"
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24 level="fatal"
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25 description="Error in the R script." />
3
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26 </stdio>
5
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27 <version_command>
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28 <![CDATA[
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29 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: ")")"
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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30 ]]>
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31 </version_command>
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32 <command>
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33 <![CDATA[
1
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34 mkdir ./html_out &&
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35 #import json
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36 Rscript '$__tool_directory__/dexseq.R'
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37 -o '$dexseq_out'
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38 -p \${GALAXY_SLOTS:-4}
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39 #set $temp_factor_names = list()
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40 #for $factor in $rep_factorName:
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41 #set $temp_factor = list()
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42 #set $count_files1 = list()
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43 #for $file in $factor.countFiles1:
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44 $count_files1.append(str($file))
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45 #end for
5
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46 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
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47
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48 #set $count_files2 = list()
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49 #for $file in $factor.countFiles2:
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50 $count_files2.append(str($file))
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51 #end for
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52 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
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53 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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54 #end for
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55 -f '#echo json.dumps(temp_factor_names)#'
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56 -a $gtf
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57 -c $fdr_cutoff
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58
0
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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 $htmlreport
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65 &&
7
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66 cp -r ./html_out/* '$htmlreport.extra_files_path'
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67 #end if
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68
0
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69 ]]>
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70 </command>
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71 <inputs>
3
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72 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
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73 <repeat name="rep_factorName" title="Factor" min="1">
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74 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
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75 help="Only letters, numbers and underscores will be retained in this field">
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76 <sanitizer>
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77 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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78 </sanitizer>
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79 </param>
5
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80 <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
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81 help="Only letters, numbers and underscores will be retained in this field">
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82 <sanitizer>
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83 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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84 </sanitizer>
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85 </param>
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86 <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
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87
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88 <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
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89 help="Only letters, numbers and underscores will be retained in this field">
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90 <sanitizer>
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91 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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92 </sanitizer>
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93 </param>
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94 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
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95 </repeat>
4
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96 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
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97 label="Visualise the analysis results?"
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98 help="Output an additional HTML file." />
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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>
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102 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" />
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103 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
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104 <filter>report is True</filter>
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105 </data>
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106 </outputs>
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107 <tests>
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108 <test>
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109 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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110 <repeat name="rep_factorName">
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111 <param name="factorName" value="condition"/>
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112 <param name="factorLevel1" value="knockdown"/>
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113 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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114 <param name="factorLevel2" value="control"/>
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115 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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116 </repeat>
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117 <repeat name="rep_factorName">
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118 <param name="factorName" value="libtype"/>
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119 <param name="factorLevel1" value="singleend"/>
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120 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
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121 <param name="factorLevel2" value="pairedend"/>
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122 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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123 </repeat>
4
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124 <param name="report" value="False"/>
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125 <param name="fdr_cutoff" value="0.05"/>
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126 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
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127 </test>
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128 </tests>
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129 <help>
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130 <![CDATA[
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131 .. class:: infomark
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132
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133 **What it does**
0
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134
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135 Inference of differential exon usage in RNA-Seq.
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136
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137
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138 **Inputs**
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139
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140 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
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141 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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142 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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143 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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144 You need to select appropriate count table from your history for each factor level.
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145
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146 The following table gives some examples of factors and their levels:
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147
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148 ========= ============== ===============
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149 Factor Factor level 1 Factor level 2
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150 --------- -------------- ---------------
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151 condition Knockdown Wildtype
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152 --------- -------------- ---------------
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153 treatment Treated Untreated
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154 --------- -------------- ---------------
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155 timePoint Day4 Day1
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156 --------- -------------- ---------------
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157 SeqType SingleEnd PairedEnd
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158 --------- -------------- ---------------
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159 Gender Female Male
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160 ========= ============== ===============
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161
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162 *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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163
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164 **Output**
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165
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166 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
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167
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168 ====== ==========================================================
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169 Column Description
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170 ------ ----------------------------------------------------------
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171 1 Gene and exon Identifiers
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172 2 group/gene identifier
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173 3 feature/exon identifier
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174 4 mean of the counts across samples in each feature/exon
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175 5 exon dispersion estimate
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176 6 LRT statistic
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177 7 LRT p-value
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178 8 BH adjusted p-values
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179 9 exon usage coefficient factorLevel 2
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180 10 exon usage coefficient factorLevel 1
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181 11 relative exon usage fold changes
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182 12 GRanges object of the coordinates of the exon/feature
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183 13 matrix of integer counts, of each column containing a sample
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184 14 list of transcripts overlapping with the exon
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185 ====== ==========================================================
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186
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187
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188 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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189 ]]>
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190 </help>
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191 <citations>
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192 <citation type="doi">10.1101/gr.133744.111</citation>
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193 </citations>
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194 </tool>