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annotate deseq2.xml @ 16:a7bf54ecfa9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7
author iuc
date Thu, 22 Sep 2016 05:49:41 -0400
parents d856341e03c8
children 24930eeff731
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a7bf54ecfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7
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1 <tool id="deseq2" name="DESeq2" version="2.1.8.4">
0
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2 <description>Determines differentially expressed features from count tables</description>
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3 <requirements>
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4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
a7bf54ecfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7
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6 <requirement type="package" version="2.17.0">r-gplots</requirement>
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7 <requirement type="package" version="0.2.15">r-rjson</requirement>
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8 <requirement type="package" version="1.10.1">bioconductor-deseq2</requirement>
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9 </requirements>
6
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10 <stdio>
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11 <regex match="Execution halted"
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12 source="both"
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13 level="fatal"
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14 description="Execution halted." />
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15 <regex match="Error in"
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16 source="both"
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17 level="fatal"
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18 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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19 <regex match="Fatal error"
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20 source="both"
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21 level="fatal"
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22 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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23 </stdio>
2
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24 <version_command>
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25 <![CDATA[
6
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26 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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27 ]]>
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28 </version_command>
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29 <command>
2
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30 <![CDATA[
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31 R -e 'library(DESeq2); sink("DESEQ2_ROOT_PATH"); cat(file.path(find.package("DESeq2"),"script","deseq2.R"))' &&
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32
0
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33 #import json
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34 Rscript \$(cat DESEQ2_ROOT_PATH)
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35 -o "$deseq_out"
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36 #if $pdf:
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37 -p "$plots"
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38 #end if
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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 #for $level in $factor.rep_factorLevel:
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43 #set $count_files = list()
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44 #for $file in $level.countsFile:
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45 $count_files.append(str($file))
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46 #end for
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47 $temp_factor.append( {str($level.factorLevel): $count_files} )
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48 #end for
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49 $temp_factor.reverse()
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50 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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51 #end for
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52 -f '#echo json.dumps(temp_factor_names)#'
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53 -t "$fit_type"
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54 #if $outlier_replace_off:
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55 -a
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56 #end if
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57 #if $outlier_filter_off:
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58 -b
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59 #end if
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60 #if $auto_mean_filter_off:
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61 -c
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62 #end if
0
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63 #if $many_contrasts:
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64 -m
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65 #end if
2
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66 ]]>
0
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67 </command>
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68 <inputs>
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69 <repeat name="rep_factorName" title="Factor" min="1">
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70 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
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71 help="Only letters, numbers and underscores will be retained in this field">
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72 <sanitizer>
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73 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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74 </sanitizer>
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75 </param>
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76 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
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77 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level"
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78 help="Only letters, numbers and underscores will be retained in this field">
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79 <sanitizer>
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80 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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81 </sanitizer>
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82 </param>
6
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83 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
0
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84 </repeat>
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85 </repeat>
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86 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
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87 label="Visualising the analysis results"
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88 help="output an additional PDF files" />
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89 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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90 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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91 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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92 <param name="fit_type" type="select" label="Fit type">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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93 <option value="1" selected="true">parametric</option>
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94 <option value="2">local</option>
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95 <option value="3">mean</option>
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96 </param>
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97 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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98 label="Turn off outliers replacement (only affects with >6 replicates)"
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99 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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100 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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101 or normalization factor for that sample" />
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102 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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103 label="Turn off outliers filtering (only affects with >2 replicates)"
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104 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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105 filter genes which contain a Cook’s distance above a cutoff" />
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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106 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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107 label="Turn off independent filtering"
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108 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
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109 </inputs>
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110 <outputs>
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111 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">
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112 <filter>many_contrasts is False</filter>
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113 </data>
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114 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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115 <filter>many_contrasts is True</filter>
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116 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
0
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117 </collection>
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118 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
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119 <filter>pdf == True</filter>
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120 </data>
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121 </outputs>
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122 <tests>
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123 <test>
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124 <repeat name="rep_factorName">
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125 <param name="factorName" value="Treatment"/>
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126 <repeat name="rep_factorLevel">
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127 <param name="factorLevel" value="Treated"/>
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128 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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129 </repeat>
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130 <repeat name="rep_factorLevel">
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131 <param name="factorLevel" value="Untreated"/>
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132 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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133 </repeat>
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134 </repeat>
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135 <param name="pdf" value="no"/>
16
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136 <output name="deseq_out" file="deseq2_out.tab" compare="sim_size" delta="1000"/>
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137 <output name="deseq_out_filtered" file="deseq2_out_filtered.tab" compare="sim_size" delta="1000"/>
0
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138 </test>
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139 </tests>
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140 <help>
2
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141 <![CDATA[
0
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142 .. class:: infomark
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143
15
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144 **What it does**
0
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145
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146 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution
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147
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148
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149 **Inputs**
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150
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151 DESeq2_ takes count tables that generated from the htseq-count as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. You also input several secondary factors that might 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. You need to select appropriate count table from your history for each factor level.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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152
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153 The following table gives some examples of factors and their levels:
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154
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155 ========= ============== ===============
15
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156 Factor Factor level 1 Factor level 2
0
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157 --------- -------------- ---------------
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158 Treatment Treated Untreated
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159 --------- -------------- ---------------
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160 Condition Knockdown Wildtype
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161 --------- -------------- ---------------
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162 TimePoint Day4 Day1
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163 --------- -------------- ---------------
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164 SeqType SingleEnd PairedEnd
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165 --------- -------------- ---------------
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166 Gender Female Male
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167 ========= ============== ===============
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168
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169 *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 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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170
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171 **Output**
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172
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173 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
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174
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175 ====== ==========================================================
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176 Column Description
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177 ------ ----------------------------------------------------------
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178 1 Gene Identifiers
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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179 2 mean normalised counts, averaged over all samples from both conditions
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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180 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
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181 4 standard error estimate for the log2 fold change estimate
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182 5 Wald statistic
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183 6 p value for the statistical significance of this change
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184 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
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185 which controls false discovery rate (FDR)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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186 ====== ==========================================================
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187
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188
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189 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
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190 ]]>
0
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191 </help>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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192 <citations>
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193 <citation type="doi">10.1186/s13059-014-0550-8</citation>
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194 </citations>
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195 </tool>