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annotate diffbind.xml @ 24:15bbd86c6c7b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
author iuc
date Thu, 19 Apr 2018 17:15:24 -0400
parents 393393c58c35
children 09aabce86f5a
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15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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1 <tool id="diffbind" name="DiffBind" version="2.6.6.2">
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2 <description> differential binding analysis of ChIP-Seq peak data</description>
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3 <requirements>
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4 <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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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 <stdio>
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9 <regex match="Execution halted"
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10 source="both"
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11 level="fatal"
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12 description="Execution halted." />
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13 <regex match="Input-Error 01"
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14 source="both"
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15 level="fatal"
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16 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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17 <regex match="Error in"
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18 source="both"
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19 level="fatal"
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20 description="An undefined error occured, please check your input carefully and contact your administrator." />
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21 </stdio>
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22 <version_command><![CDATA[
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23 echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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24 ]]></version_command>
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25 <command><![CDATA[
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26 #import re
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27 #import json
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28
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29 ## Adapted from DESeq2 wrapper
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30 #set $temp_factor_names = list()
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31 #set $temp_factor = list()
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32
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33 #for $g in $rep_group:
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35 #set $peak_files = list()
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36 #set $bam_files = list()
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37 #set $bam_controls = list()
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38
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39 #for $file in $g.peaks:
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40 #set $file_name = re.sub('[^\w\-\s]', '_', str($file.element_identifier))
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41 ln -s '${file}' ${g.groupName}-${file_name}-peaks.bed &&
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42 $peak_files.append(str($g.groupName) + '-' + $file_name + '-peaks.bed')
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43 #end for
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44
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45 #for $bam in $g.bamreads:
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46 #set $bam_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
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47 ln -s '${bam}' ${bam_name}-bamreads.bam &&
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48 ln -s ${bam.metadata.bam_index} ${bam_name}-bamreads.bai &&
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49 $bam_files.append($bam_name + '-bamreads.bam')
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50 #end for
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51
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52 $temp_factor.append( {str($g.groupName): $peak_files} )
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53 $temp_factor.append( {str($g.groupName): $bam_files} )
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54
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55 #if str( $g.bamcontrol ) != 'None':
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56 #for $ctrl in $g.bamcontrol:
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57 #set $ctrl_name = re.sub('[^\w\-\s]', '_', str($ctrl.element_identifier))
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58 ln -s '${ctrl}' ${g.groupName}-${ctrl_name}-bamcontrol.bam &&
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59 ln -s ${ctrl.metadata.bam_index} ${g.groupName}-${ctrl_name}-bamcontrol.bai &&
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60 $bam_controls.append(str($g.groupName) + '-' + $ctrl_name + '-bamcontrol.bam')
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61 #end for
23
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62 $temp_factor.append( {str($g.groupName): $bam_controls} )
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63 #end if
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64
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65 #end for
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66
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67 $temp_factor.reverse()
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68 $temp_factor_names.append(["Condition", $temp_factor])
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69
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70
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71 Rscript '$__tool_directory__/diffbind.R'
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72
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73 -i '#echo json.dumps(temp_factor_names)#'
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74 -o '$outfile'
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75 -t $th
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76 -f $out.format
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77 -p '$plots'
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78
23
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79 #if $scorecol:
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80 -n "$scorecol"
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81 #end if
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82 #if $lowerbetter:
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83 -l "$lowerbetter"
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84 #end if
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85 #if $summits:
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86 -s "$summits"
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87 #end if
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88
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89 #if $out.binding_matrix:
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90 -b
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91 #end if
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92
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93 #if $out.rdata:
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94 -r
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95 #end if
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96
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97 #if $out.analysis_info:
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98 -a
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99 #end if
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100
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101 #if $out.rscript:
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102 && cp '$__tool_directory__/diffbind.R' '$rscript'
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103 #end if
22
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104 ]]>
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105 </command>
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106 <inputs>
24
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107 <repeat name="rep_group" title="Group" min="2" max="2" default="2">
23
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108 <param name="groupName" type="text" label="Name"
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109 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups in total must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">
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110 <sanitizer>
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111 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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112 </sanitizer>
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113 <validator type="empty_field" />
23
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114 </param>
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115 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
24
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116 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM file" help="Specify the Read BAM file used in the Peak calling."/>
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117 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM file" help="If specifying a control BAM file, all samples are required to specify one, see Help section below."/>
22
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118 </repeat>
23
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119
24
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120 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)">
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121 <sanitizer>
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122 <valid initial="string.digits"/>
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123 </sanitizer>
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124 </param>
23
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125 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" />
24
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126 <param name="summits" type="integer" min="0" optional="True" label="Summits" help="Extend peaks Nbp up- and downstream of the summit. For punctate peaks it is advisable to extend (e.g. 250bp), see the DiffBind User Guide">
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127 <sanitizer>
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128 <valid initial="string.digits"/>
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129 </sanitizer>
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130 </param>
23
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131 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/>
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132
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133 <!-- Output Options -->
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134 <section name="out" expanded="false" title="Output Options">
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135 <param name="format" type="select" label="Output Format">
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136 <option value="bed">BED</option>
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137 <option value="gff">GFF</option>
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138 <option value="wig">WIG</option>
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139 </param>
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140 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" />
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141 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" />
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142 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/>
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143 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
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144 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/>
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145 </section>
22
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146 </inputs>
23
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147
22
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148 <outputs>
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149 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}: Differentially bound sites" />
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150 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots">
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151 <filter>out['pdf']</filter>
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152 </data>
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153 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix">
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154 <filter>out['binding_matrix']</filter>
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155 </data>
23
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156 <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file">
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157 <filter>out['rdata']</filter>
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158 </data>
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159 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
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160 <filter>out['rscript']</filter>
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161 </data>
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162 <data name="analysis_info" format="txt" from_work_dir="DiffBind_analysis_info.txt" label="${tool.name} on ${on_string}: Analysis info">
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163 <filter>out['analysis_info']</filter>
22
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164 </data>
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165 </outputs>
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166
22
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167 <tests>
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168 <test expect_num_outputs="6">
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169 <repeat name="rep_group">
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170 <param name="groupName" value="Resistant"/>
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171 <param name="peaks" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
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172 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
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173 </repeat>
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174 <repeat name="rep_group">
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175 <param name="groupName" value="Responsive"/>
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176 <param name="peaks" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
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177 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
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178 </repeat>
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179 <param name="scorecol" value="5" />
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180 <param name="pdf" value="True" />
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181 <param name="binding_matrix" value="True" />
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182 <param name="rdata" value="True" />
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183 <param name="rscript" value="True"/>
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184 <param name="analysis_info" value="True"/>
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185 <output name="outfile" value="out_diffbind.tab" />
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186 <output name="plots" value="out_plots.pdf" compare="sim_size" />
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187 <output name="binding_matrix" value="out_binding.matrix" />
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188 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/>
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189 <output name="rscript" value="out_rscript.txt"/>
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190 <output name="analysis_info" value="out_analysis_info.txt" compare="sim_size" >
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191 <assert_contents>
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192 <has_text text="SessionInfo"/>
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193 </assert_contents>
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194 </output>
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195 </test>
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196 </tests>
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197 <help><![CDATA[
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198
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199 .. class:: infomark
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200
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201 **What it does**
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202
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203 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific
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204 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and
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205 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously,
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206 representing different ChIP experiments (antibodies, transcription factor and/or histone
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207 marks, experimental conditions, replicates) as well as managing the results of multiple peak
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208 callers.
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209
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210 The primary emphasis of DiffBind is on identifying sites that are differentially bound
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211 between two sample groups. It includes functions to support the processing of peak sets,
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212 including overlapping and merging peak sets, counting sequencing reads overlapping intervals
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213 in peak sets, and identifying statistically significantly differentially bound sites based on
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214 evidence of binding affinity (measured by differences in read densities). To this end it uses
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215 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages
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216 edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a
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217 set of standardized plots to aid in binding analysis.
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218
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219 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of
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220 examples: the first focusing on the core task of obtaining differentially bound sites based on
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221 affinity data, the second working through the main plotting routines, the third discussing the
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222 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail,
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223 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
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224 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
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225
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226 Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).
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227
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228 -----
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229
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230 **Inputs**
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231
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232 DiffBind works primarily with peaksets, which are sets of genomic intervals representing
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233 candidate protein binding sites. Each interval consists of a chromosome, a start and end
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234 position, and usually a score of some type indicating confidence in, or strength of, the peak.
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235 Associated with each peakset are metadata relating to the experiment from which the peakset
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236 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to
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237 be associated with each peakset (one for the ChIP data, and optionally another representing
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238 a control sample)
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239
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240 **Groups**
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241
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242 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above.
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243
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244 Example:
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245
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246 ============= =============
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247 **Sample** **Group**
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248 ------------- -------------
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249 BT4741 Resistant
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250 BT4742 Resistant
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251 MCF71 Responsive
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252 MCF72 Responsive
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253 ============= =============
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254
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255
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256 **Peak files**
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257
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258 Result of your Peak calling experiment in bed format, one file for each sample is required. The peak caller, format and score column can be specified in the tool form above. The default settings expect narrowPeak bed format, which has the score in the 8th column (-log10pvalue), and can be output from MACS2.
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259
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260 Example:
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261
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262 ======= ======= ======= =============== ==============
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263 1 2 3 4 **5 (Score)**
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264 ======= ======= ======= =============== ==============
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265 chr18 215562 216063 peak_16037 56.11
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266 chr18 311530 312105 peak_16038 222.49
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267 chr18 356656 357315 peak_16039 92.06
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268 chr18 371110 372092 peak_16040 123.86
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269 chr18 395116 396464 peak_16041 1545.39
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270 chr18 399014 400382 peak_16042 1835.19
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271 chr18 499134 500200 peak_16043 748.32
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272 chr18 503518 504552 peak_16044 818.30
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273 chr18 531672 532274 peak_16045 159.30
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274 chr18 568326 569282 peak_16046 601.11
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275 ======= ======= ======= =============== ==============
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276
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277 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required.
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278 * Optional: Control BAM file representing a control dataset. If used, has to be specified for all samples. Note that the DiffBind authors say control reads are best utilized prior to running DiffBind, at the peak calling stage (e.g. with MACS2) and in blacklists, see this `Bioconductor post`_.
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279
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280 -----
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281
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282 **Outputs**
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283
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284 This tool outputs
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285
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286 * a table of differentially bound sites
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287
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288 Optionally, under **Output Options** you can choose to output
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289
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290 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots)
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291 * a binding affinity matrix
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292 * the R script used by this tool
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293 * an RData file of the R objects generated
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294 * a text file with information on the analysis (number of Intervals, FriP scores, method used)
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295
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296 **Differentially Bound Sites**
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297
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298 Example:
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299
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300 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ========
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301 seqnames start end width strand Conc Conc_Responsive Conc_Resistant Fold p.value **FDR**
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302 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ========
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303 chr18 394600 396513 1914 \* 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21
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304 chr18 111567 112005 439 \* 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06
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305 chr18 346464 347342 879 \* 5 5.77 3.24 2.52 6.51e-06 0.00303
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306 chr18 399014 400382 1369 \* 7.62 7 8.05 -1.04 1.04e-05 0.00364
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307 chr18 371110 372102 993 \* 4.63 3.07 5.36 -2.3 8.1e-05 0.0226
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308 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ========
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309
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310 Columns contain the following data:
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311
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312 * **seqnames**: Chromosome name
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313 * **start**: Start position of site
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314 * **end**: End position of site
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315 * **width**: Length of site
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316 * **strand**: Strand
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317 * **Conc**: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)
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318 * **Responsive**: Mean concentration over the first (e.g. Responsive) group
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319 * **Resistant**: Mean concentration over second (e.g. Resistant) group
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320 * **Fold**: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group.
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321 * **p.value**: P-value confidence measure for identifying these sites as differentially bound
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322 * **FDR**: a multiple testing corrected FDR p-value
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323
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324
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325 **Binding Affinity Matrix**
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326
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327 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent
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328 differential analysis.
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329
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330 Example:
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331
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332 ===== ====== ====== ========= ========= ========== ==========
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333 CHR START END MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2
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334 ===== ====== ====== ========= ========= ========== ==========
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335 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945
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336 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095
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337 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434
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338 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040
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339 chr18 346464 347342 75.63583 40.96941 21.00995 16.80796
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340 chr18 356560 357362 11.55547 14.70696 57.77737 53.57538
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341 chr18 371110 372102 8.403982 9.454479 81.93882 82.98932
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342 chr18 394600 396513 56.72687 43.07040 510.5419 438.0575
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343 chr18 399014 400382 156.5241 117.6557 558.8648 496.8854
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344 chr18 498906 500200 767.9138 278.3819 196.4430 181.7361
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345 ===== ====== ====== ========= ========= ========== ==========
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346
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347 -----
22
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348
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349 **More Information**
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350
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351 Generally, processing data with DiffBind involves five phases:
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352
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353 #. Reading in peaksets
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354 #. Occupancy analysis
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355 #. Counting reads
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356 #. Differential binding affinity analysis
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357 #. Plotting and reporting
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358
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359
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360 **Reading in peaksets**:
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361
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362 The first step is to read in a set of peaksets and associated
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363 metadata. Peaksets are derived either from ChIP-Seq peak callers, such as **MACS2**, or using some other criterion (e.g. genomic windows, or all the promoter regions
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364 in a genome). A single experiment can have more than
22
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365 one associated peakset; e.g. if multiple peak callers are used for comparison purposes
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366 each sample would have more than one line in the sample sheet. Once the peaksets
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367 are read in, a merging function finds all overlapping peaks and derives a single set of
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368 unique genomic intervals covering all the supplied peaks (a consensus peakset for the
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369 experiment).
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370
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371 **Occupancy analysis**:
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372
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373 Peaksets, especially those generated by peak callers, provide
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374 an insight into the potential occupancy of the protein being ChIPed for at specific
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375 genomic loci. After the peaksets have been loaded, it can be useful to perform some
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376 exploratory plotting to determine how these occupancy maps agree with each other,
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377 e.g. between experimental replicates (re-doing the ChIP under the same conditions),
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378 between different peak callers on the same experiment, and within groups of samples
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379 representing a common experimental condition. DiffBind provides functions to enable
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380 overlaps to be examined, as well as functions to determine how well similar samples
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381 cluster together. Beyond quality control, the product of an occupancy analysis may be
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382 a consensus peakset, representing an overall set of candidate binding sites to be used
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383 in further analysis.
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384
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385 **Counting reads**:
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386
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387 Once a consensus peakset has been derived, DiffBind can use the
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388 supplied sequence read files to count how many reads overlap each interval for each
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389 unique sample. The peaks in the consensus peakset may be re-centered and trimmed
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390 based on calculating their summits (point of greatest read overlap) in order to provide
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391 more standardized peak intervals. The final result of counting is a binding affinity matrix
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392 containing a (normalized) read count for each sample at every potential binding site.
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393 With this matrix, the samples can be re-clustered using affinity, rather than occupancy,
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394 data. The binding affinity matrix is used for QC plotting as well as for subsequent
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395 differential analysis.
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396
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397 **Differential binding affinity analysis**:
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398
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399 The core functionality of DiffBind is the
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400 differential binding affinity analysis, which enables binding sites to be identified that
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401 are statistically significantly differentially bound between sample groups. To accomplish
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402 this, first a contrast (or contrasts) is established, dividing the samples into groups to
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403 be compared. Next the core analysis routines are executed, by default using DESeq2.
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404 This will assign a p-value and FDR to each candidate binding site indicating confidence
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405 that they are differentially bound.
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406
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407 **Plotting and reporting**:
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408
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409 Once one or more contrasts have been run, DiffBind provides
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410 a number of functions for reporting and plotting the results. MA plots give an
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411 overview of the results of the analysis, while correlation heatmaps and PCA plots show
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412 how the groups cluster based on differentially bound sites. Boxplots show the distribution
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413 of reads within differentially bound sites corresponding to whether they gain or
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414 lose affinity between the two sample groups. A reporting mechanism enables differentially
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415 bound sites to be extracted for further processing, such as annotation, motif, and
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416 pathway analyses.
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417
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418 -----
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419
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420 **References**
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421
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422 DiffBind Authors: Rory Stark, Gordon Brown (2011)
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423 Wrapper authors: Bjoern Gruening, Pavankumar Videm
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424
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425 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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426 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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427 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
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428 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/
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429
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430 ]]>
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431 </help>
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432 <citations>
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433 <citation type="doi">doi:10.1038/nature10730</citation>
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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434 </citations>
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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435 </tool>