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1 <tool id="macs2_peakcalling" name="MACS2" version="2.0.10">
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2 <description>Model-based Analysis of ChIP-Seq</description>
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3 <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command>
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4 <version_command>macs2 --version</version_command>
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5 <inputs>
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6 <!--experiment name and option of selecting paired or single end will always be present-->
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7 <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/>
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8
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9 <!--select one of the 7 major commands offered by macs2-->
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10 <conditional name="major_command">
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11 <param name="major_command_selector" type="select" label="Select action to be performed">
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12 <option value="callpeak">Peak Calling</option>
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13 <!--<option value="filterdup">filterdup</option>
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14 <option value="randsample">randsample</option>-->
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15 <option value="bdgcmp">Compare .bdg Files</option>
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16 <!--<option value="bdgdiff">bdgdiff</option>
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17 <option value="bdgpeakcall">bdgpeakcall</option>
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18 <option value="bdgbroadcall">bdgbroadcall</option>-->
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19 </param>
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20 <!--callpeak option of macs2-->
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21 <when value="callpeak">
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22 <!--may need to add a few more formats at later time-->
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23 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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24 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
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25 <param name="gsize" type="integer" label="Effective genome size" value="2700000000" help="Human: 3.3e+9, Mouse: 3.0e+9, Fly: 1.9e+8, Worm: 1.3e+8 (--gsize)"/>
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26 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/>
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27 <param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="True" falsevalue="False" checked="False"/>
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28 <param name="bdg" label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" type="boolean" truevalue="-B" falsevalue="" checked="False" help="files located in html report"/>
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29
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30 <conditional name="pq_options">
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31 <param name="pq_options_selector" type="select" label="Select p-value or q-value" help="default uses q-value">
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32 <option value="qvalue">q-value</option>
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33 <option value="pvalue">p-value</option>
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34 </param>
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35 <when value="pvalue">
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36 <param name="pvalue" type="float" label="p-value cutoff for peak detection" value="1e-2" help="default: 1e-2 (--pvalue)"/>
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37 </when>
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38 <when value="qvalue">
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39 <param name="qvalue" type="float" label="q-value cutoff for peak detection" value="5e-2" help="default: 5e-2 (--qvalue)"/>
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40 </when>
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41 </conditional>
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42 <conditional name="advanced_options">
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43 <param name="advanced_options_selector" type="select" label="Display advanced options">
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44 <option value="off">Hide</option>
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45 <option value="on">Display</option>
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46 </param>
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47 <when value="on">
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48 <param name="mfoldlo" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)" value="10" help="(--mfold)"/>
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49 <param name="mfoldhi" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" value="30" help="(--mfold)"/>
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50 <param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming (--nolambda)"/>
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51 <conditional name="broad_options">
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52 <param name="broad_options_selector" type="select" label="Composite broad regions" help="put nearby highly enriched regions into a broad region with loose cutoff (--broad)">
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53 <option value="nobroad" selected="true">No broad regions</option>
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54 <option value="broad">Broad regions</option>
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55 </param>
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56 <when value="broad">
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57 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
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58 </when>
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59 <when value="nobroad"/>
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60 </conditional>
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61 </when>
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62 <when value="off">
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63 <!--display nothing-->
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64 </when>
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65 </conditional>
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66 <conditional name="nomodel_type">
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67 <param name="nomodel_type_selector" type="select" label="Build Model">
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68 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option>
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69 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option>
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70 </param>
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71 <when value="nomodel">
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72 <param name="shiftsize" type="integer" label="Arbitrary shift size in bp" value="100" help="(--shiftsize)"/>
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73 </when>
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74 </conditional>
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75 </when>
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76
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77 <!--callpeak option of macs2-->
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78 <when value="bdgcmp">
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79 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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80 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
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81 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" help="default: 0.00001 (-p)"/>
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82
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83 <conditional name="bdgcmp_options">
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84 <param name="bdgcmp_options_selector" type="select" label="Select action to be performed">
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85 <option value="ppois">ppois</option>
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86 <option value="qpois">qpois</option>
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87 <option value="subtract">subtract</option>
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88 <option value="logFE">logFE</option>
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89 <option value="FE">FE</option>
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90 <option value="logLR">logLR</option>
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91 </param>
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92 </conditional>
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93 </when>
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94 </conditional>
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95 </inputs>
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96
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97 <outputs>
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98 <!--callpeaks output-->
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99 <data name="output_bed_file" format="bed" label="${tool.name}: callpeak on ${on_string} (peaks: bed)">
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100 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
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101 </data>
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102 <data name="output_extra_files" format="html" label="${tool.name}: callpeak on ${on_string} (html report)">
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103 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
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104 </data>
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105 <data name="output_peaks_file" format="xls" label="${tool.name}: callpeak on ${on_string} (peaks: xls)">
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106 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
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107 </data>
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108 <data name="output_narrowpeaks_file" format="txt" label="${tool.name}: callpeak on ${on_string} (peaks: encodePeak)">
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109 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
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110 </data>
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111 <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name}: callpeak on ${on_string} (peaks: interval)">
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112 <filter>major_command['xls_to_interval'] is True</filter>
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113 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
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114 </data>
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115 <data name="output_xls_to_interval_negative_peaks_file" format="interval" label="${tool.name}: callpeak on ${on_string} (negative peaks: interval)">
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116 <filter>major_command['xls_to_interval'] is True</filter>
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117 <filter>major_command['input_control_file1'] is not None</filter>
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118 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
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119 </data>
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120 <!--bdgcmp output-->
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121 <data name="output_bdgcmp_file" format="bdg" label="${tool.name}: bdgcmp on ${on_string} (bdg)">
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122 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter>
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123 </data>
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124 </outputs>
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125 <configfiles>
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126
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127 <configfile name="outputs_file"><%
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128 import json
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129 %>
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130 ##=======================================================================================
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131 #set $__outputs = { 'command':str( $major_command.major_command_selector ) }
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132 #if str( $major_command.major_command_selector ) == 'callpeak':
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133 #set $__outputs['output_bed_file'] = str( $output_bed_file )
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134 #set $__outputs['output_extra_file'] = str( $output_extra_files )
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135 #set $__outputs['output_extra_file_path'] = str( $output_extra_files.files_path )
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136 #set $__outputs['output_peaks_file'] = str( $output_peaks_file )
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137 #set $__outputs['output_narrowpeaks_file'] = str( $output_narrowpeaks_file )
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138 #set $__outputs['output_xls_to_interval_peaks_file'] = str( $output_xls_to_interval_peaks_file )
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139 #set $__outputs['output_xls_to_interval_negative_peaks_file'] = str( $output_xls_to_interval_negative_peaks_file )
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140 #end if
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141 ##=======================================================================================
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142 #if str( $major_command.major_command_selector ) == 'bdgcmp':
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143 #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file )
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144 #end if
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145
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146 ${ json.dumps( __outputs ) }
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147 </configfile>
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148 <configfile name="options_file"><%
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149 import json
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150 %>
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151 ##=======================================================================================
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152 #set $__options = { 'experiment_name':str( $experiment_name ) }
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153 ##treatment/tag input files and format
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154 #set $__options['input_chipseq'] = [ str( $major_command.input_chipseq_file1 ) ]
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155 #set $__options['format'] = $major_command.input_chipseq_file1.extension.upper()
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156
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157 ##control/input files
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158 #set $__options['input_control'] = []
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159 #if str( $major_command.input_control_file1 ) != 'None':
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160 #set $_hole = __options['input_control'].append( str( $major_command.input_control_file1 ) )
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161 #end if
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162
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163 #if str( $major_command.major_command_selector ) == 'callpeak':
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164 #set $__options['command'] = str( "callpeak" )
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165 #set $__options['gsize'] = int( $major_command.gsize )
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166 #set $__options['bw'] = str( $major_command.bw )
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167 #set $__options['bdg'] = str( $major_command.bdg )
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168 #set $__options['xls_to_interval'] = str( $major_command.xls_to_interval )
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169
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170 ##advanced options
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171 #if str( $major_command.advanced_options.advanced_options_selector ) == 'on':
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172 #set $__options['mfoldlo'] = int( $major_command.advanced_options.mfoldlo )
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173 #set $__options['mfoldhi'] = int( $major_command.advanced_options.mfoldhi )
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174 #set $__options['nolambda'] = str( $major_command.advanced_options.nolambda )
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175 #if str($major_command.advanced_options.broad_options.broad_options_selector) == 'broad'
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176 #set $__options['broad_cutoff'] = str($major_command.advanced_options.broad_options.broad_cutoff)
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177 #end if
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178 #else:
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179 #set $__options['mfoldlo'] = int( "10" )
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180 #set $__options['mfoldhi'] = int( "30" )
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181 #set $__options['nolambda'] = str( "" )
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182 #end if
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183
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184 ##enable xls file options
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185 ##if str( $major_command.xls_to_interval ) == 'create':
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186 ##set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) }
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187 ##end if
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188
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189 ##pq value select options
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190 #if str( $major_command.pq_options.pq_options_selector ) == 'qvalue':
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191 #set $__options['qvalue'] = str( $major_command.pq_options.qvalue )
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192 #else:
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193 #set $__options['pvalue'] = str( $major_command.pq_options.pvalue )
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194 #end if
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195
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196 ##model options
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197 #if str( $major_command.nomodel_type.nomodel_type_selector ) == 'nomodel':
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198 #set $__options['nomodel'] = str( $major_command.nomodel_type.shiftsize )
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199 #end if
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200 #end if
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201 ##=======================================================================================
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202 #if str( $major_command.major_command_selector ) == 'bdgcmp':
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203 #set $__options['command'] = str( "bdgcmp" )
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204 #set $__options['pseudocount'] = float( str( $major_command.pseudocount ) )
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205 #set $__options['m'] = str( $major_command.bdgcmp_options.bdgcmp_options_selector )
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206 #end if
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207 ##=======================================================================================
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208
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209 ${ json.dumps( __options ) }
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210 </configfile>
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211 </configfiles>
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212 <tests>
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213 <!--none yet for macs2-->
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214 </tests>
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215 <help>
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216 **What it does**
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217
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218 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
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219 is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
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220 identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
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221 binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
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222
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223 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
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224
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225 ------
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226
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227 **Usage**
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228
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229 **Peak Calling**: Main MACS2 Function to Call peaks from alignment results.
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230
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231 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
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232
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233
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234 ------
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235
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236 **Citation**
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237
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238 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
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239
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240 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
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241 </help>
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242 </tool>
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