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annotate diffbind.xml @ 23:393393c58c35 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
author iuc
date Sat, 07 Apr 2018 15:45:03 -0400
parents 51f0f4df83c2
children 15bbd86c6c7b
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393393c58c35 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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1 <tool id="diffbind" name="DiffBind" version="2.6.6.1">
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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 intput carefully and contact your administrator." />
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21 </stdio>
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22 <version_command><![CDATA[
23
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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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34
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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 $temp_factor_names.append([str($factorName), $temp_factor])
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69
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70
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71 Rscript '$__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>
23
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107 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Condition). One factor must be entered and there must be two or more groups. NOTE: Please only use letters, numbers or underscores.">
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108 <sanitizer>
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109 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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110 </sanitizer>
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111 </param>
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112 <repeat name="rep_group" title="Group" min="2" default="2">
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113 <param name="groupName" type="text" label="Name"
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114 help="Name of group that the peak files belong to (e.g. Resistant or Responsive). NOTE: Please only use letters, numbers or underscores (case sensitive).">
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115 <sanitizer>
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116 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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117 </sanitizer>
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118 </param>
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119 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
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120 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM file" help="Specify the Read BAM file used for Peak calling."/>
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121 <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."/>
22
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122 </repeat>
23
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123
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124 <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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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" />
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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 <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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128
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129 <!-- Output Options -->
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130 <section name="out" expanded="false" title="Output Options">
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131 <param name="format" type="select" label="Output Format">
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132 <option value="bed">BED</option>
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133 <option value="gff">GFF</option>
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134 <option value="wig">WIG</option>
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135 </param>
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136 <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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137 <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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138 <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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139 <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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140 <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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141 </section>
22
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142 </inputs>
23
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143
22
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144 <outputs>
23
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145 <data name="outfile" format="bed" label="${tool.name} on ${on_string}: Differentially bound sites">
22
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146 <change_format>
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147 <when input="format" value="wig" format="wig" />
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148 <when input="format" value="gff" format="gff" />
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149 </change_format>
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150 </data>
23
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151 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots">
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152 <filter>out['pdf']</filter>
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153 </data>
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154 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix">
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155 <filter>out['binding_matrix']</filter>
22
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156 </data>
23
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157 <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file">
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158 <filter>out['rdata']</filter>
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159 </data>
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160 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
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161 <filter>out['rscript']</filter>
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162 </data>
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163 <data name="analysis_info" format="txt" from_work_dir="DiffBind_analysis_info.txt" label="${tool.name} on ${on_string}: Analysis info">
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164 <filter>out['analysis_info']</filter>
22
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165 </data>
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166 </outputs>
23
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167
22
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168 <tests>
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169 <test expect_num_outputs="6">
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170 <param name="factorName" value="Condition"/>
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171 <repeat name="rep_group">
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172 <param name="groupName" value="Resistant"/>
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173 <param name="peaks" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
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174 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
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175 </repeat>
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176 <repeat name="rep_group">
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177 <param name="groupName" value="Responsive"/>
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178 <param name="peaks" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
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179 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
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180 </repeat>
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181 <param name="scorecol" value="5" />
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182 <param name="pdf" value="True" />
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183 <param name="binding_matrix" value="True" />
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184 <param name="rdata" value="True" />
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185 <param name="rscript" value="True"/>
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186 <param name="analysis_info" value="True"/>
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187 <output name="outfile" value="out_diffbind.bed" />
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188 <output name="plots" value="out_plots.pdf" compare="sim_size" />
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189 <output name="binding_matrix" value="out_binding.matrix" />
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190 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/>
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191 <output name="rscript" value="out_rscript.txt"/>
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192 <output name="analysis_info" value="out_analysis_info.txt" compare="sim_size" >
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193 <assert_contents>
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194 <has_text text="SessionInfo"/>
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195 </assert_contents>
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196 </output>
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197 </test>
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198 </tests>
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199 <help><![CDATA[
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200
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201 .. class:: infomark
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202
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203 **What it does**
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204
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205 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific
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206 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and
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207 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously,
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208 representing different ChIP experiments (antibodies, transcription factor and/or histone
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209 marks, experimental conditions, replicates) as well as managing the results of multiple peak
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210 callers.
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211
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212 The primary emphasis of DiffBind is on identifying sites that are differentially bound
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213 between two sample groups. It includes functions to support the processing of peak sets,
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214 including overlapping and merging peak sets, counting sequencing reads overlapping intervals
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215 in peak sets, and identifying statistically significantly differentially bound sites based on
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216 evidence of binding affinity (measured by differences in read densities). To this end it uses
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217 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages
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218 edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a
22
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219 set of standardized plots to aid in binding analysis.
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220
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221 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of
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222 examples: the first focusing on the core task of obtaining differentially bound sites based on
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223 affinity data, the second working through the main plotting routines, the third discussing the
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224 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail,
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225 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
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226 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
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227
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228 Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).
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229
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230 -----
22
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231
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232 **Inputs**
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233
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234 DiffBind works primarily with peaksets, which are sets of genomic intervals representing
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235 candidate protein binding sites. Each interval consists of a chromosome, a start and end
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236 position, and usually a score of some type indicating confidence in, or strength of, the peak.
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237 Associated with each peakset are metadata relating to the experiment from which the peakset
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238 was derived. Additionally, files containing mapped sequencing reads (generally .bam files) can
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239 be associated with each peakset (one for the ChIP data, and optionally another representing
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240 a control sample)
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241
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242 **Sample Information**
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243
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244 You have to specify your sample information in the tool form above, where Factor is the groups you want to compare (e.g Resistant and Responsive).
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245
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246 Example:
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247
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248 ============= =============
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249 **SampleID** **Group**
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250 ------------- -------------
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251 BT4741 Resistant
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252 BT4742 Resistant
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253 MCF71 Responsive
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254 MCF72 Responsive
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255 ============= =============
22
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256
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257
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258 **Peak files**
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259
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260 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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261
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262 Example (MACS.xls file in bed format):
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263
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264 ======= ======= ======= =============== ==============
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265 1 2 3 4 **5 (Score)**
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266 ======= ======= ======= =============== ==============
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267 chr18 215562 216063 MACS_peak_16037 56.11
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268 chr18 311530 312105 MACS_peak_16038 222.49
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269 chr18 356656 357315 MACS_peak_16039 92.06
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270 chr18 371110 372092 MACS_peak_16040 123.86
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271 chr18 395116 396464 MACS_peak_16041 1545.39
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272 chr18 399014 400382 MACS_peak_16042 1835.19
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273 chr18 499134 500200 MACS_peak_16043 748.32
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274 chr18 503518 504552 MACS_peak_16044 818.30
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275 chr18 531672 532274 MACS_peak_16045 159.30
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276 chr18 568326 569282 MACS_peak_16046 601.11
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277 ======= ======= ======= =============== ==============
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278
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279 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required.
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280 * 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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281
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282 -----
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283
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284 **Outputs**
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285
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286 This tool outputs
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287
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288 * differentially bound sites in BED, WIG or GFF format
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289
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290 Optionally, under **Output Options** you can choose to output
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291
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292 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots)
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293 * a binding affinity matrix
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294 * the R script used by this tool
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295 * an RData file of the R objects generated
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296 * a text file with information on the analysis (number of Intervals, FriP scores, method used)
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297
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298 **Differentially Bound Sites**
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299
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300 As output format you can choose BED, GFF, WIG.
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301
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302 Example - BED format:
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303
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304 ======== ====== ====== ===== ====== ===== =============== ============== ======= ======== ========
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305 seqnames start end width strand Conc Conc_Responsive Conc_Resistant Fold p.value **FDR**
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306 ======== ====== ====== ===== ====== ===== =============== ============== ======= ======== ========
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307 chr18 394600 396513 1914 * 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21
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308 chr18 111567 112005 439 * 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06
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309 chr18 346464 347342 879 * 5 5.77 3.24 2.52 6.51e-06 0.00303
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310 chr18 399014 400382 1369 * 7.62 7 8.05 -1.04 1.04e-05 0.00364
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311 chr18 371110 372102 993 * 4.63 3.07 5.36 -2.3 8.1e-05 0.0226
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312 ======== ====== ====== ===== ====== ===== =============== ============== ======= ======== ========
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313
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314 Columns contain the following data:
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315
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316 * **1st**: Chromosome name
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317 * **2nd**: Start position of site
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318 * **3rd**: End position of site
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319 * **4th**: Length of site
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320 * **5th**: Strand
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321 * **6th**: 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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322 * **7th**: Mean concentration over the first (e.g. Resistant) group
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323 * **8th**: Mean concentration over second (e.g. Responsive) group
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324 * **9th**: Fold shows the difference in mean concentrations between the two groups (e.g. Resistant - Responsive), 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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325 * **10th**: P-value confidence measure for identifying these sites as differentially bound
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326 * **11th**: a multiple testing corrected FDR p-value
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327
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328
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329 **Binding Affinity Matrix**
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330
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331 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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332 differential analysis.
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333
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334 Example:
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335
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336 ===== ====== ====== ================ ================ ================ ================
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337 CHR START END MCF7_ER_1.bed MCF7_ER_2.bed BT474_ER_1.bed BT474_ER_2.bed
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338 ===== ====== ====== ================ ================ ================ ================
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339 chr18 111567 112005 137.615208000375 59.878372946728 29.4139375878664 19.9594576489093
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340 chr18 189223 189652 19.9594576489093 12.6059732519427 11.5554754809475 23.110950961895
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341 chr18 215232 216063 11.5554754809475 15.7574665649284 31.5149331298568 72.4843461986707
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342 chr18 311530 312172 17.8584621069189 11.5554754809475 54.6258840917518 43.0704086108043
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343 chr18 346464 347342 75.6358395116564 40.9694130688139 21.0099554199046 16.8079643359236
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344 chr18 356560 357362 11.5554754809475 14.7069687939332 57.7773774047375 53.5753863207566
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345 chr18 371110 372102 8.40398216796182 9.45447993895705 81.9388261376278 82.989323908623
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346 chr18 394600 396513 56.7268796337423 43.0704086108043 510.541916703681 438.05757050501
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347 chr18 399014 400382 156.524167878289 117.655750351465 558.864814169461 496.885445680743
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348 chr18 498906 500200 767.913870597511 278.381909313735 196.443083176108 181.736114382174
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349 ===== ====== ====== ================ ================ ================ ================
22
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350
23
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351 -----
22
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352
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353 **More Information**
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354
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355 Generally, processing data with DiffBind involves five phases:
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356
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357 #. Reading in peaksets
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358 #. Occupancy analysis
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359 #. Counting reads
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360 #. Differential binding affinity analysis
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361 #. Plotting and reporting
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362
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363
23
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364 **Reading in peaksets**:
22
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365
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366 The first step is to read in a set of peaksets and associated
23
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367 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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368 in a genome). A single experiment can have more than
22
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369 one associated peakset; e.g. if multiple peak callers are used for comparison purposes
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370 each sample would have more than one line in the sample sheet. Once the peaksets
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371 are read in, a merging function finds all overlapping peaks and derives a single set of
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372 unique genomic intervals covering all the supplied peaks (a consensus peakset for the
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373 experiment).
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374
23
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375 **Occupancy analysis**:
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376
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377 Peaksets, especially those generated by peak callers, provide
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378 an insight into the potential occupancy of the protein being ChIPed for at specific
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379 genomic loci. After the peaksets have been loaded, it can be useful to perform some
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380 exploratory plotting to determine how these occupancy maps agree with each other,
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381 e.g. between experimental replicates (re-doing the ChIP under the same conditions),
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382 between different peak callers on the same experiment, and within groups of samples
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383 representing a common experimental condition. DiffBind provides functions to enable
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384 overlaps to be examined, as well as functions to determine how well similar samples
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385 cluster together. Beyond quality control, the product of an occupancy analysis may be
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386 a consensus peakset, representing an overall set of candidate binding sites to be used
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387 in further analysis.
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388
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389 **Counting reads**:
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390
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391 Once a consensus peakset has been derived, DiffBind can use the
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392 supplied sequence read files to count how many reads overlap each interval for each
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393 unique sample. The peaks in the consensus peakset may be re-centered and trimmed
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394 based on calculating their summits (point of greatest read overlap) in order to provide
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395 more standardized peak intervals. The final result of counting is a binding affinity matrix
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396 containing a (normalized) read count for each sample at every potential binding site.
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397 With this matrix, the samples can be re-clustered using affinity, rather than occupancy,
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398 data. The binding affinity matrix is used for QC plotting as well as for subsequent
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399 differential analysis.
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400
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401 **Differential binding affinity analysis**:
22
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402
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403 The core functionality of DiffBind is the
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404 differential binding affinity analysis, which enables binding sites to be identified that
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405 are statistically significantly differentially bound between sample groups. To accomplish
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406 this, first a contrast (or contrasts) is established, dividing the samples into groups to
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407 be compared. Next the core analysis routines are executed, by default using DESeq2 .
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408 This will assign a p-value and FDR to each candidate binding site indicating confidence
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409 that they are differentially bound.
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410
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411 **Plotting and reporting**:
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412
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413 Once one or more contrasts have been run, DiffBind provides
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414 a number of functions for reporting and plotting the results. MA plots give an
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415 overview of the results of the analysis, while correlation heatmaps and PCA plots show
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416 how the groups cluster based on differentially bound sites. Boxplots show the distribution
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417 of reads within differentially bound sites corresponding to whether they gain or
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418 lose affinity between the two sample groups. A reporting mechanism enables differentially
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419 bound sites to be extracted for further processing, such as annotation, motif, and
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420 pathway analyses.
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421
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422 -----
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423
22
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424 **References**
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425
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426 DiffBind Authors: Rory Stark, Gordon Brown (2011)
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427 Wrapper authors: Bjoern Gruening, Pavankumar Videm
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428
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429 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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430 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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431 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
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432 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/
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433
22
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434 ]]>
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435 </help>
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436 <citations>
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437 <citation type="doi">doi:10.1038/nature10730</citation>
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438 </citations>
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439 </tool>