Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 5:28a2181df3b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
author iuc
date Thu, 08 Oct 2015 16:49:40 -0400
parents 7069d55968fb
children 469c0d7489bd
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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">
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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>
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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." />
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16 <regex match="Error in"
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17 source="both"
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18 level="fatal"
5
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19 description="An undefined error occured, please check your input carefully and contact your administrator." />
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20 <regex match="Error:"
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21 source="both"
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22 level="fatal"
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23 description="Error in the R script." />
3
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24 </stdio>
5
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25 <version_command>
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26 <![CDATA[
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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27 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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28 ]]>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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29 </version_command>
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30 <command>
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31 <![CDATA[
1
36fe30ece23b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e2ab82632ee80aa2347545b2f21235d851b8c36a-dirty
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32 mkdir ./html_out &&
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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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33 #import json
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
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34 Rscript $__tool_directory__/dexseq.R
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35 -o "$dexseq_out"
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36 -p \${GALAXY_SLOTS:-4}
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37 #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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38 #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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39 #set $temp_factor = list()
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40 #set $count_files1 = list()
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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41 #for $file in $factor.countFiles1:
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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42 $count_files1.append(str($file))
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43 #end for
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44 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
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45
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46 #set $count_files2 = list()
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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47 #for $file in $factor.countFiles2:
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48 $count_files2.append(str($file))
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49 #end for
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50 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
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51 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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52 #end for
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53 -f '#echo json.dumps(temp_factor_names)#'
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54 -a $gtf
4
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55 -c $fdr_cutoff
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56
0
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57 #if $report:
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58 -r ./html_out
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59 &&
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60 mkdir $htmlreport.extra_files_path
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61 &&
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62 cp ./html_out/testForDEU.html $htmlreport
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63 &&
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64 cp -r ./html_out/* $htmlreport.extra_files_path
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65 #end if
4
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66
0
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67 ]]>
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68 </command>
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69 <inputs>
3
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70 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
0
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71 <repeat name="rep_factorName" title="Factor" min="1">
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72 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
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73 help="Only letters, numbers and underscores will be retained in this field">
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74 <sanitizer>
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75 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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76 </sanitizer>
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77 </param>
5
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78 <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
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79 help="Only letters, numbers and underscores will be retained in this field">
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80 <sanitizer>
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81 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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82 </sanitizer>
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83 </param>
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84 <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
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85
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86 <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
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87 help="Only letters, numbers and underscores will be retained in this field">
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88 <sanitizer>
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89 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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90 </sanitizer>
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91 </param>
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92 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
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93 </repeat>
4
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94 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
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95 label="Visualise the analysis results?"
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96 help="Output an additional HTML file." />
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97 <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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98 </inputs>
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99 <outputs>
4
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100 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" />
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101 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
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102 <filter>report is True</filter>
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103 </data>
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104 </outputs>
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105 <tests>
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106 <test>
5
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107 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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108 <repeat name="rep_factorName">
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109 <param name="factorName" value="condition"/>
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110 <param name="factorLevel1" value="knockdown"/>
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111 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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112 <param name="factorLevel2" value="control"/>
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113 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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114 </repeat>
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115 <repeat name="rep_factorName">
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116 <param name="factorName" value="libtype"/>
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117 <param name="factorLevel1" value="singleend"/>
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118 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
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119 <param name="factorLevel2" value="pairedend"/>
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120 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
0
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121 </repeat>
4
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122 <param name="report" value="False"/>
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123 <param name="fdr_cutoff" value="0.05"/>
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124 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
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125 </test>
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126 </tests>
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127 <help>
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128 <![CDATA[
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129 .. class:: infomark
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130
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131 **What it does**
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132
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133 Inference of differential exon usage in RNA-Seq.
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134
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135
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136 **Inputs**
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137
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138 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
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139 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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140 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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141 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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142 You need to select appropriate count table from your history for each factor level.
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143
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144 The following table gives some examples of factors and their levels:
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145
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146 ========= ============== ===============
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147 Factor Factor level 1 Factor level 2
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148 --------- -------------- ---------------
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149 condition Knockdown Wildtype
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150 --------- -------------- ---------------
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151 treatment Treated Untreated
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152 --------- -------------- ---------------
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153 timePoint Day4 Day1
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154 --------- -------------- ---------------
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155 SeqType SingleEnd PairedEnd
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156 --------- -------------- ---------------
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157 Gender Female Male
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158 ========= ============== ===============
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159
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160 *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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161
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162 **Output**
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163
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164 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
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165
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166 ====== ==========================================================
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167 Column Description
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168 ------ ----------------------------------------------------------
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169 1 Gene and exon Identifiers
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170 2 group/gene identifier
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171 3 feature/exon identifier
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172 4 mean of the counts across samples in each feature/exon
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173 5 exon dispersion estimate
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174 6 LRT statistic
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175 7 LRT p-value
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176 8 BH adjusted p-values
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177 9 exon usage coefficient factorLevel 2
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178 10 exon usage coefficient factorLevel 1
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179 11 relative exon usage fold changes
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180 12 GRanges object of the coordinates of the exon/feature
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181 13 matrix of integer counts, of each column containing a sample
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182 14 list of transcripts overlapping with the exon
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183 ====== ==========================================================
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184
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185
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186 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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187 ]]>
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188 </help>
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189 <citations>
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190 <citation type="doi">10.1101/gr.133744.111</citation>
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191 </citations>
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192 </tool>