Mercurial > repos > iuc > macs2

annotate macs2_callpeak.xml @ 63:25e46cf1ee36 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
author iuc
date Sat, 02 Apr 2022 21:36:50 +0000
parents 1ac88e46ee0f
children
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25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
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1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Call peaks from alignment results</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macs2_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 </expand>
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command><![CDATA[
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12 #import re
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13
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14 @home_dir@
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15 #set $temp_stderr = 'macs2_stderr'
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16
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17 (macs2 callpeak
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19 ## Treatment File(s)
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21 #if str($treatment.t_multi_select) == "Yes":
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22 -t ${ ' '.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) }
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23 #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file[0].element_identifier))
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24 #else
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25 -t '$treatment.input_treatment_file'
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26 #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file.element_identifier))
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27 #end if
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29 --name $identifier
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30
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31 ## Control File(s)
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33 #if str($control.c_select) == "Yes":
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34 #if str($control.c_multiple.c_multi_select) == "Yes":
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35 -c ${ ' '.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) }
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36 #else
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37 -c '$control.c_multiple.input_control_file'
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38 #end if
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39 #end if
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41 --format $format
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42
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43 @effective_genome_size@
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44
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45 ## advanced options
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47 $advanced_options.nolambda
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48 $advanced_options.to_large
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49 $advanced_options.spmr
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51 #if $advanced_options.ratio:
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52 --ratio $advanced_options.ratio
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53 #end if
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55 #if $advanced_options.slocal:
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56 --slocal $advanced_options.slocal
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57 #end if
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59 #if $advanced_options.llocal:
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60 --llocal $advanced_options.llocal
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61 #end if
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62
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63 #if $advanced_options.broad_options.broad_options_selector == "broad":
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64 --broad
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65 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
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66 #else
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67 $advanced_options.broad_options.call_summits
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68 #end if
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69
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70 #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
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71 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
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72 #else
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73 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
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74 #end if
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75
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76 --d-min $advanced_options.d_min
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77 --buffer-size $advanced_options.buffer_size
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78
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79 ## With --bdg two additional output files will be generated.
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80 #if "bdg" in str($outputs).split(','):
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81 --bdg
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82 #end if
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83
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84 ## cutoff selection
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85 #if str( $cutoff_options.cutoff_options_selector ) == "qvalue":
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86 --qvalue '${ cutoff_options.qvalue }'
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87 #elif str( $cutoff_options.cutoff_options_selector ) == "pvalue":
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88 #if str($cutoff_options.pvalue).strip() != "":
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89 --pvalue '${ cutoff_options.pvalue }'
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90 #end if
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91 #end if
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92
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93 ## model options
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94 #if $nomodel_type.nomodel_type_selector == "nomodel":
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95 --nomodel
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96 --extsize '${ nomodel_type.extsize }'
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97 --shift '${ nomodel_type.shift}'
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98 #else
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99 --mfold '${nomodel_type.mfold_lower}' '${nomodel_type.mfold_upper}'
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100
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101 #if $nomodel_type.band_width:
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102 --bw '${nomodel_type.band_width}'
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103 #end if
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104 #end if
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105
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106 2>&1 > $temp_stderr)
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107 #if "peaks_tabular" in str($outputs).split(','):
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108 &&
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109 cp ${identifier}_peaks.xls '${ output_tabular }'
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110 #end if
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111
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112 ## run R to create pdf from model script
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113 #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE":
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114 &&
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115 Rscript ${identifier}_model.r > ${identifier}_model.r.log
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116 #end if
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117
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118 #if 'html' in str($outputs).split(','):
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119 ## if output files exists, move them to the files_path and create a html result page linking to them
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120 &&
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121 (
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122 count=`ls -1 ${identifier}* 2>/dev/null | wc -l`;
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123 if [ \$count != 0 ];
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124 then
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125 mkdir '${ output_extra_files.files_path }' &&
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126 cp -r ${identifier}* '${ output_extra_files.files_path }' &&
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127 python '$__tool_directory__/dir2html.py'
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128 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }';
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129 fi;
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130 )
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131 #end if
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132 &&
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133 exit_code_for_galaxy=\$? &&
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134 cat $temp_stderr 2>&1 &&
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135 (exit \$exit_code_for_galaxy)
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136 ]]></command>
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137 <inputs>
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138 <conditional name="treatment">
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139 <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" >
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140 <option value="No" selected="True">No</option>
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141 <option value="Yes">Yes</option>
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142 </param>
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143 <when value="No" >
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144 <param name="input_treatment_file" argument="-t" type="data" format="bam,bed" label="ChIP-Seq Treatment File" />
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145 </when>
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146 <when value="Yes">
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147 <param name="input_treatment_file" argument="-t" type="data" format="bam,bed" multiple="true" label="ChIP-Seq Treatment File" />
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148 </when>
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149 </conditional>
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150
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151 <conditional name="control">
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152 <param name="c_select" type="select" label="Do you have a Control File?" >
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153 <option value="Yes">Yes</option>
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154 <option value="No" selected="True">No</option>
52
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155 </param>
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156 <when value="Yes">
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157 <conditional name="c_multiple">
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158 <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" >
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159 <option value="No" selected="True">No</option>
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160 <option value="Yes">Yes</option>
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161 </param>
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162 <when value="No" >
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163 <param name="input_control_file" argument="-c" type="data" format="bam,bed" label="ChIP-Seq Control File" />
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164 </when>
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165 <when value="Yes">
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166 <param name="input_control_file" argument="-c" type="data" format="bam,bed" multiple="true" label="ChIP-Seq Control File" />
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167 </when>
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168 </conditional>
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169 </when>
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170 <when value="No" />
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171 </conditional>
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172
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173 <param argument="--format" type="select" label="Format of Input Files" help="For Paired-end BAM (BAMPE) the 'Build model step' will be ignored and the real fragments will be used for each template defined by leftmost and rightmost mapping positions. Default: Single-end BAM">
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174 <option value="BAM" selected="True">Single-end BAM</option>
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175 <option value="BAMPE">Paired-end BAM</option>
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176 <option value="BED">Single-end BED</option>
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177 </param>
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178
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179 <expand macro="conditional_effective_genome_size" />
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180
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181 <conditional name="nomodel_type">
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182 <param name="nomodel_type_selector" type="select" label="Build Model">
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183 <option value="nomodel">Do not build the shifting model (--nomodel)</option>
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184 <option value="create_model" selected="true">Build the shifting model</option>
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185 </param>
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186 <when value="create_model">
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187 <param name="mfold_lower" type="integer" value="5" label="Set lower mfold bound" help="Select the lower region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be higher than lower limit (--mfold). Default: 5" />
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188 <param name="mfold_upper" type="integer" value="50" label="Set upper mfold bound" help="Select the upper region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than the upper limit (--mfold). Default: 50"/>
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189 <param name="band_width" argument="--bw" type="integer" value="300"
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190 label="Band width for picking regions to compute fragment size"
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191 help=" You can set this parameter as the medium fragment size expected from sonication or size selection. Default: 300" />
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192 </when>
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193 <when value="nomodel">
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194 <param argument="--extsize" type="integer" value="200" label="Set extension size" help="The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3-prime; end, then pile them up. It is exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5-prime-to-3-prime direction to middle of fragment by 0.5 d, then extended to both direction with 0.5 d. This is equivalent to say each read is extended towards 5-prime-to-3-prime into a d size fragment. --extsize (this option) and --shift (the option below) can be combined when necessary. See --shift option below. Default: 200."/>
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195 <param argument="--shift" type="integer" value="0" label="Set shift size" help="(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5-prime) towards 5-prime-to-3-prime direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3-prime-to-5-prime direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * 0.5 of --extsize (option above) together with --extsize option for detecting enriched cutting loci such as certain DNAseI-Seq datasets. Note, you can't set values other than 0 if format is paired-end data (BAMPE). Default: 0"/>
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196 </when>
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197 </conditional>
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198
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199 <conditional name="cutoff_options">
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200 <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
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201 <option value="qvalue" selected="true">q-value</option>
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202 <option value="pvalue">p-value</option>
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203 </param>
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204 <when value="pvalue">
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205 <param argument="--pvalue" type="float" value="" label="p-value cutoff for peak detection" help="Default: not set"/>
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206 </when>
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207 <when value="qvalue">
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208 <param argument="--qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection" help="The q-value (minimum FDR) cutoff to call significant regions. Default is 0.05. For broad marks, you can try 0.05 as cutoff. Q-values are calculated from p-values using Benjamini-Hochberg procedure"/>
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209 </when>
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210 </conditional>
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211
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212 <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built">
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213 <option value="peaks_tabular">Peaks as tabular file (compatible wih MultiQC)</option>
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214 <option value="summits">Peak summits</option>
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215 <option value="bdg" >Scores in bedGraph files (--bdg)</option>
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216 <option value="html">Summary page (html)</option>
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217 <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
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218 </param>
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219
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220 <section name="advanced_options" title="Advanced Options">
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221 <param name="to_large" argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
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222 label="When set, scale the small sample up to the bigger sample"
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223 help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. Default: No"/>
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224 <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false"
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225 label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming. Default: No"/>
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226 <param name="spmr" argument="--SPMR" type="boolean" truevalue="--SPMR" falsevalue="" checked="false"
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227 label="Save signal per million reads for fragment pileup profiles"
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228 help="Requires 'Scores in bedGraph files (--bdg)' output to be selected. Default: No"/>
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229 <param argument="--ratio" type="float" optional="true"
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230 label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
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231 help="Default: ignore"/>
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232 <param name="slocal" type="integer" optional="True" label="The small nearby region in basepairs to calculate dynamic lambda"
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233 help="This is used to capture the bias near the peak summit region. Invalid if there is no control data. If you set this to 0, MACS will skip slocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--slocal). Default: 1000"/>
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234 <param argument="--llocal" type="integer" optional="True" label="The large nearby region in basepairs to calculate dynamic lambda"
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235 help="This is used to capture the surround bias. If you set this to 0, MACS will skip llocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. Default: 10000"/>
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236 <conditional name="broad_options">
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237 <param name="broad_options_selector" argument="--broad" type="select"
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238 label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff">
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239 <option value="nobroad" selected="true">No broad regions</option>
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240 <option value="broad">broad regions</option>
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241 </param>
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242 <when value="broad">
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243 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
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244 help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
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245 </when>
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246 <when value="nobroad">
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247 <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
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248 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/>
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249 </when>
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250 </conditional>
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251 <expand macro="keep_duplicates" />
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252 <expand macro="fragment_size"/>
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253 <expand macro="buffer_size"/>
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254 </section>
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255 </inputs>
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256 <outputs>
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257 <!--callpeaks output-->
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258 <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
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259 <filter> outputs and 'peaks_tabular' in outputs</filter>
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260 </data>
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261 <data name="output_broadpeaks" format="bed" from_work_dir="*_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
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262 <filter>
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263 ((
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264 advanced_options['broad_options']['broad_options_selector'] == "broad"
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265 ))
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266 </filter>
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267 </data>
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268 <data name="output_gappedpeaks" format="bed" from_work_dir="*_peaks.gappedPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
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269 <filter>
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270 ((
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271 advanced_options['broad_options']['broad_options_selector'] == "broad"
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272 ))
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273 </filter>
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274 </data>
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275 <data name="output_narrowpeaks" format="bed" from_work_dir="*_peaks.narrowPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
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276 <filter>
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277 ((
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278 advanced_options['broad_options']['broad_options_selector'] == "nobroad"
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279 ))
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280 </filter>
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281 </data>
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282 <data name="output_summits" format="bed" from_work_dir="*_summits.bed" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
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283 <filter>outputs and 'summits' in outputs</filter>
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284 </data>
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285 <data name="output_plot" format="pdf" from_work_dir="*_model.pdf" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (plot)">
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286 <filter>
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287 ((
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288 outputs and 'pdf' in outputs and
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289 nomodel_type['nomodel_type_selector'] == "create_model" and
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290 format != "BAMPE"
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291 ))
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292 </filter>
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293 </data>
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294 <data name="output_treat_pileup" format="bedgraph" from_work_dir="*_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
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295 <filter>outputs and 'bdg' in outputs</filter>
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296 </data>
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297 <data name="output_control_lambda" format="bedgraph" from_work_dir="*_control_lambda.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
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298 <filter>outputs and 'bdg' in outputs</filter>
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299 </data>
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300 <data name="output_extra_files" format="html" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (html report)">
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301 <filter>outputs and 'html' in outputs</filter>
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302 </data>
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303 </outputs>
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304 <tests>
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305 <test expect_num_outputs="5">
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306 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
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307 <param name="c_select" value="Yes"/>
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308 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
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309 <param name="format" value="BED" />
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310 <param name="cutoff_options_selector" value="qvalue"/>
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311 <param name="qvalue" value="0.05"/>
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312 <param name="band_width" value="300"/>
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313 <param name="outputs" value="peaks_tabular,bdg,html"/>
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314 <param name="effective_genome_size_options_selector" value="user_defined" />
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315 <param name="gsize" value="3300000000" />
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316 <param name="lower" value="5" />
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317 <param name="upper" value="50" />
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318 <assert_command>
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319 <has_text text="--buffer-size"/>
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320 <has_text text="--d-min"/>
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321 </assert_command>
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322 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
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323 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
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324 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/>
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325 <output name="output_extra_files">
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326 <assert_contents>
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327 <has_text text="Additional output created by MACS2" />
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328 </assert_contents>
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329 </output>
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330 </test>
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331 <!-- Ensure pdf can be output -->
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332 <test expect_num_outputs="2">
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333 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
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334 <param name="c_select" value="Yes"/>
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335 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
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336 <param name="format" value="BED" />
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337 <param name="cutoff_options_selector" value="qvalue"/>
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338 <param name="qvalue" value="0.05"/>
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339 <param name="band_width" value="300"/>
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340 <param name="outputs" value="pdf"/>
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341 <param name="effective_genome_size_options_selector" value="user_defined" />
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342 <param name="gsize" value="3300000000" />
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343 <param name="lower" value="5" />
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344 <param name="upper" value="50" />
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345 <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/>
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346 </test>
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347 <!-- Ensure BAMPE works -->
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348 <test expect_num_outputs="1">
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349 <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/>
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350 <param name="format" value="BAMPE" />
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351 <param name="effective_genome_size_options_selector" value="user_defined"/>
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352 <param name="gsize" value="3300000000"/>
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353 <param name="nomodel_type_selector" value="nomodel"/>
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354 <param name="nolambda" value="True"/>
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355 <!-- we select PDF as output, but since we are in BAMPE mode, this will not ignored and the expect_num_outputs stays one. -->
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356 <param name="outputs" value="pdf"/>
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357 <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
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358 </test>
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359 </tests>
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360 <help><![CDATA[
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361 .. class:: infomark
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362
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363 **What it does**
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364
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365 **callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments. It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.
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366
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367 -----
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368
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369 **Inputs**
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370
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371 MACS can be used for ChIP-Seq data (Treatment) alone, or with a Control sample with the increase of specificity (recommended).
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372
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373 A Treatment File is the only REQUIRED parameter for MACS. The file can be in BAM or BED format and this tool will autodetect the format using the first treatment file provided as input. If you have more than one alignment file per sample, you can select to pool them above. MACS can pool files together e.g. as `-t A B C` for treatment or `-c A B C` for control.
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374
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375 Both single-end and paired-end mapping results can be input and you can specify if the data is from paired-end reads above. Paired-end mapping results can be input to MACS as a single BAM file, and just the left mate (5' end) tag will be automatically kept. However, when paired-end format (BAMPE) is specified, MACS will use the real fragments inferred from alignment results for reads pileup.
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376
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377 *Effective Genome Size*
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378
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379 PLEASE assign this parameter to fit your needs!
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380
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381 It's the mappable genome size or effective genome size which is defined as the genome size which can be sequenced. Because of the repetitive features on the chromsomes, the actual mappable genome size will be smaller than the original size, about 90% or 70% of the genome size. The default hs -- 2.7e9 is recommended for UCSC human hg18 assembly. Here are all precompiled parameters for effective genome size from the MACS2_ website:
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382
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383 hs: 2.7e9
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384 mm: 1.87e9
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385 ce: 9e7
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386 dm: 1.2e8
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387
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388 Or see the **deepTools** website for updated information on calculating `Effective Genome Size`_.
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389
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390 -----
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391
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392 **Outputs**
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393
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394 This tool produces a BED file of narrowPeaks as default output. It can also produce additional outputs, which can be selected under the **Additional Outputs** option above.
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395
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396 * **a BED file of peaks** (default)
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397 * a tabular file of peaks (compatible wih MultiQC)
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398 * a BED file of peak summits
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399 * two bedGraph files of scores, for treatment pileup and control lambda
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400 * a HTML summary page
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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401 * a PDF plot (if model is built)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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402 * a BED file of broad peaks (if **Composite broad regions** is selected under Advanced Options)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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403 * a BED file of gapped peaks (if **Composite broad regions** is selected under Advanced Options)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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404
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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405 **Peaks BED File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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406
53
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407 The default output is the narrowPeak BED file (BED6+4 format). This contains the peak locations, together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser.
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408
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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409 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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410
60
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411 ======= ========= ======= ============= ==== === ======= ======== ======= =======
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412 1 2 3 4 5 6 7 8 9 **10**
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413 ======= ========= ======= ============= ==== === ======= ======== ======= =======
58
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414 chr1 840081 840400 treat1_peak_1 69 . 4.89872 10.50944 6.91052 158
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415 chr1 919419 919785 treat1_peak_2 87 . 5.85158 12.44148 8.70936 130
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416 chr1 937220 937483 treat1_peak_3 66 . 4.87632 10.06728 6.61759 154
60
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417 ======= ========= ======= ============= ==== === ======= ======== ======= =======
52
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418
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419 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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420
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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421 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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422 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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423 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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424 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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425 * **5th**: integer score for display in genome browser (e.g. UCSC)
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426 * **6th**: strand, either "." (=no strand) or "+" or "-"
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427 * **7th**: fold-change
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428 * **8th**: -log10pvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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429 * **9th**: -log10qvalue
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430 * **10th**: relative summit position to peak start
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431
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432
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433 **Peaks tabular File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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434
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435 A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions. This file is compatible with **MultiQC**.
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436
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437 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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438
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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439 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
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440 **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)** **fold_enrichment** **-log10(qvalue)** **name**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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441 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
58
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442 chr1 840082 840400 319 840240 4.00 10.50944 4.89872 6.91052 treat1_peak_1
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443 chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 treat1_peak_2
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444 chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 treat1_peak_3
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445 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
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446
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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447 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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448
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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449 * **chr**: chromosome name
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450 * **start**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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451 * **end**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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452 * **length**: length of peak region
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453 * **abs_summit**: absolute peak summit position
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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454 * **pileup**: pileup height at peak summit
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455 * **-log10(pvalue)**: -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10)
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456 * **fold_enrichment**: fold enrichment for this peak summit against random Poisson distribution with local lambda
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457 * **-log10(qvalue)**: -log10(qvalue) at peak summit
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458 * **name**: name of peak
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459
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460 *Note that these tabular file coordinates are 1-based which is different than the 0-based BED format (compare the start values in the BED and tabular Example above)*
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461
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462
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463 **Summits BED File**
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464
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465 A BED file which contains the peak summits locations for every peaks. The 5th column in this file is -log10qvalue, the same as in the Peaks BED file. If you want to find the motifs at the binding sites, this file is recommended. The file can be loaded directly to UCSC genome browser. Remove the beginning track line if you want to analyze it by other tools.
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466
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467 Example:
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468
60
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469 ======= ========= ======= ============= =======
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470 1 2 3 4 **5**
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471 ======= ========= ======= ============= =======
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472 chr1 840239 840240 treat1_peak_1 6.91052
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473 chr1 919549 919550 treat1_peak_2 8.70936
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474 chr1 937374 937375 treat1_peak_3 6.61759
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475 ======= ========= ======= ============= =======
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476
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477 Columns contain the following data:
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478
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479 * **1st**: chromosome name
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480 * **2nd**: start position of peak
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481 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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482 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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483 * **5th**: -log10qvalue
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diff changeset
484
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
485
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
486 **BedGraph Files**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
487
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
488 MACS2 will output two kinds of bedGraph files if the --bdg option is selected under the Additional Outputs option above, which contain the scores for the treatment fragment pileup and control local lambda, respectively. BedGraph files can be imported into genome browsers, such as UCSC genome browser, or be converted into even smaller bigWig files. For more information on bedGraphs, see the `UCSC website here`_.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
489
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
490
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
491 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
492
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
493 **Treatment pileup file**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
494
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
495 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
496 1 2 3 **4**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
497 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
498 chr1 840146 840147 3.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
499 chr1 840147 840332 4.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
500 chr1 840332 840335 3.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
501 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
502
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
503
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
504 **Control lambda file**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
505
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
506 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
507 1 2 3 **4**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
508 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
509 chr1 800953 801258 0.02536
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
510 chr1 801258 801631 0.25364
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
511 chr1 801631 801885 0.99858
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
512 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
513
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
514 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
515
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
516 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
517 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
518 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
519 * **4th**: treatment pileup score or control local lambda score
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
520
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
521
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
522 **Broad peaks File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
523
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
524 If the broad option (--broad) is selected unded Advanced Options above, MACS2 will output a broadPeaks file. When this flag is on, MACS will try to composite broad regions in BED12 ( a gene-model-like format ) by putting nearby highly enriched regions into a broad region with loose cutoff. The broad region is controlled by another cutoff through --broad-cutoff. The maximum length of broad region length is 4 times of d from MACS. The broad peaks file is in BED6+3 format which is similar to the narrowPeak file, except for missing the 10th column for annotating peak summits.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
525
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
526 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
527
60
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
528 ======= ====== ====== ============= ==== === ======= ======= =======
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
529 1 2 3 4 5 6 7 8 9
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
530 ======= ====== ====== ============= ==== === ======= ======= =======
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
531 chr1 840081 840400 treat1_peak_1 52 . 4.08790 8.57605 5.21506
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
532 chr1 919419 919785 treat1_peak_2 56 . 4.37270 8.90436 5.60462
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
533 chr1 937220 937483 treat1_peak_3 48 . 4.02343 8.06676 4.86861
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
534 ======= ====== ====== ============= ==== === ======= ======= =======
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
535
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
536 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
537
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
538 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
539 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
540 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
541 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
542 * **5th**: integer score for display in genome browser (e.g. UCSC)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
543 * **6th**: strand, either "." (=no strand) or "+" or "-"
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
544 * **7th**: fold-change
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
545 * **8th**: -log10pvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
546 * **9th**: -log10qvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
547
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
548
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
549 **Gapped peaks File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
550
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
551 If the broad option (--broad) is selected unded Advanced Options above, MACS2 will also output a gappedPeaks file. The gappedPeak file is in BED12+3 format and contains both the broad region and narrow peaks. The file can be loaded directly to UCSC genome browser.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
552
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
553 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
554
60
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
555 ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
556 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
557 ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
558 chr1 840081 840400 treat1_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
559 chr1 919419 919785 treat1_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
560 chr1 937220 937483 treat1_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861
75bd115a2085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6
iuc
parents: 59
diff changeset
561 ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
562
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
563 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
564
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
565 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
566 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
567 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
568 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
569 * **5th**: 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
570 * **6th**: strand, either "." (=no strand) or "+" or "-"
53
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571 * **7th**: start of the first narrow peak in the region
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572 * **8th**: end of the peak
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573 * **9th**: RGB color key, default colour is 0
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574 * **10th**: number of blocks, including the starting 1bp and ending 1bp of broad regions
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575 * **11th**: length of each block, comma-separated values if multiple
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576 * **12th**: start of each block, comma-separated values if multiple
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577 * **13th**: fold-change
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578 * **14th**: -log10pvalue
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579 * **15th**: -log10qvalue
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580
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581 -----
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582
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583 **More Information**
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584
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585 MACS2 performs the following analysis steps:
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586
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587 * Artificially extends reads to expected fragment length, and generates coverage map along genome.
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588 * Assumes background reads are Poisson distributed. Mean of the Poisson is locally variable and is estimated from control experiment (if available) in 5Kbp or 10Kbp around examined location.
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589 * For a given location, asks do we see more reads than we would have expected from the Poisson (p < 0.00005)? If Yes, MACS2 calls a peak.
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590
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591
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592 **Tips of fine-tuning peak calling**
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593
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594 Check out these other MACS2 tools:
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595
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596 * **MACS2 bdgcmp** can be used on the callpeak bedGraph files or bedGraph files from other resources to calculate score track.
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597 * **MACS2 bdgpeakcall** can be used on the file generated from bdgcmp or bedGraph file from other resources to call peaks with given cutoff, maximum-gap between nearby mergable peaks and minimum length of peak. bdgbroadcall works similarly to bdgpeakcall, however it will output a broad peaks file in BED12 format.
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598 * Differential calling tool **MACS2 bdgdiff**, can be used on 4 bedGraph files which are scores between treatment 1 and control 1, treatment 2 and control 2, treatment 1 and treatment 2, treatment 2 and treatment 1. It will output the consistent and unique sites according to parameter settings for minimum length, maximum gap and cutoff.
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599
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600 .. class:: warningmark
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601
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602 If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options. For more information, see the MACS2_ website.
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603
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604 .. _MACS2: https://github.com/taoliu/MACS
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605 .. _`Effective Genome Size`: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
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606 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html
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607
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608 @citation@
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609 ]]></help>
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610 <expand macro="citations" />
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611 </tool>