Mercurial > repos > iuc > macs2

annotate macs2_callpeak.xml @ 14:c16dbe4e2db2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
author iuc
date Mon, 06 Aug 2018 10:41:57 -0400
parents 01cded2297b7
children c33686854b19
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1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.4" profile="17.09">
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2 <description>Call peaks from alignment results</description>
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3 <macros>
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4 <import>macs2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 </expand>
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command><![CDATA[
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11 #import re
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13 @home_dir@
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14 #set $temp_stderr = 'macs2_stderr'
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15
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16 (macs2 callpeak
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18 ## Treatment File(s)
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20 #if str($treatment.t_multi_select) == "Yes":
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21 -t ${ ' '.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) }
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22 #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file[0].element_identifier))
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23 #else
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24 -t '$treatment.input_treatment_file'
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25 #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file.element_identifier))
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26 #end if
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27
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28 --name $identifier
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30 ## Control File(s)
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32 #if str($control.c_select) == "Yes":
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33 #if str($control.c_multiple.c_multi_select) == "Yes":
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34 -c ${ ' '.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) }
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35 #else
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36 -c '$control.c_multiple.input_control_file'
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37 #end if
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38 #end if
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39
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40 --format $format
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41
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42 @effective_genome_size@
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43
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44 ## advanced options
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46 $advanced_options.nolambda
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47 $advanced_options.to_large
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49 #if $advanced_options.ratio:
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50 --ratio $advanced_options.ratio
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51 #end if
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53 #if $advanced_options.slocal:
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54 --slocal $advanced_options.slocal
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55 #end if
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57 #if $advanced_options.llocal:
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58 --llocal $advanced_options.llocal
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59 #end if
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60
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61 #if $advanced_options.broad_options.broad_options_selector == "broad":
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62 --broad
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63 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
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64 #else
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65 $advanced_options.broad_options.call_summits
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66 #end if
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67
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68 #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
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69 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
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70 #else
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71 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
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72 #end if
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73
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74
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75 ## With --bdg two additional output files will be generated.
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76 #if "bdg" in str($outputs).split(','):
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77 --bdg
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78 #end if
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79
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80 ## cutoff selection
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81 #if str( $cutoff_options.cutoff_options_selector ) == "qvalue":
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82 --qvalue '${ cutoff_options.qvalue }'
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83 #elif str( $cutoff_options.cutoff_options_selector ) == "pvalue":
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84 #if str($cutoff_options.pvalue).strip() != "":
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85 --pvalue '${ cutoff_options.pvalue }'
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86 #end if
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87 #end if
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88
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89 ## model options
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90 #if $nomodel_type.nomodel_type_selector == "nomodel":
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91 --nomodel
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92 --extsize '${ nomodel_type.extsize }'
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93 --shift '${ nomodel_type.shift}'
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94 #else
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95 --mfold '${nomodel_type.mfold_lower}' '${nomodel_type.mfold_upper}'
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97 #if $nomodel_type.band_width:
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98 --bw '${nomodel_type.band_width}'
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99 #end if
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100 #end if
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101
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102 2>&1 > $temp_stderr)
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103 #if "peaks_tabular" in str($outputs).split(','):
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104 &&
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105 cp ${identifier}_peaks.xls '${ output_tabular }'
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106 #end if
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107
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108 ## run R to create pdf from model script
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109 #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE":
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110 &&
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111 Rscript ${identifier}_model.r > ${identifier}_model.r.log
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112 #end if
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113
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114 #if 'html' in str($outputs).split(','):
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115 ## if output files exists, move them to the files_path and create a html result page linking to them
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116 &&
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117 (
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118 count=`ls -1 ${identifier}* 2>/dev/null | wc -l`;
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119 if [ \$count != 0 ];
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120 then
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121 mkdir '${ output_extra_files.files_path }' &&
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122 cp -r ${identifier}* '${ output_extra_files.files_path }' &&
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123 python '$__tool_directory__/dir2html.py'
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124 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }';
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125 fi;
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126 )
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127 #end if
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128 &&
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129 exit_code_for_galaxy=\$? &&
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130 cat $temp_stderr 2>&1 &&
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131 (exit \$exit_code_for_galaxy)
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132 ]]></command>
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133 <inputs>
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134 <conditional name="treatment">
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135 <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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136 <option value="No" selected="True">No</option>
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137 <option value="Yes">Yes</option>
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138 </param>
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139 <when value="No" >
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140 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" />
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141 </when>
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142 <when value="Yes">
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143 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Treatment File" />
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144 </when>
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145 </conditional>
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146
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147 <conditional name="control">
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148 <param name="c_select" type="select" label="Do you have a Control File?" >
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149 <option value="Yes">Yes</option>
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150 <option value="No" selected="True">No</option>
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151 </param>
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152 <when value="Yes">
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153 <conditional name="c_multiple">
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154 <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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155 <option value="No" selected="True">No</option>
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156 <option value="Yes">Yes</option>
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157 </param>
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158 <when value="No" >
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159 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" label="ChIP-Seq Control File" />
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160 </when>
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161 <when value="Yes">
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162 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Control File" />
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163 </when>
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164 </conditional>
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165 </when>
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166 <when value="No" />
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167 </conditional>
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168
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169 <param name="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 (--format). Default: Single-end BAM">
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170 <option value="BAM" selected="True">Single-end BAM</option>
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171 <option value="BAMPE">Paired-end BAM</option>
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172 <option value="BED">Single-end BED</option>
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173 </param>
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174
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175 <expand macro="conditional_effective_genome_size" />
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176
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177 <conditional name="nomodel_type">
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178 <param name="nomodel_type_selector" type="select" label="Build Model">
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179 <option value="nomodel">Do not build the shifting model (--nomodel)</option>
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180 <option value="create_model" selected="true">Build the shifting model</option>
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181 </param>
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182 <when value="create_model">
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183 <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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184 <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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185 <param name="band_width" type="integer" value="300"
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186 label="Band width for picking regions to compute fragment size"
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187 help=" You can set this parameter as the medium fragment size expected from sonication or size selection (--bw). Default: 300" />
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188 </when>
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189 <when value="nomodel">
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190 <param name="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 (--extsize)."/>
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191 <param name="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 (--shift)."/>
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192 </when>
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193 </conditional>
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194
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195 <conditional name="cutoff_options">
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196 <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
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197 <option value="qvalue" selected="true">q-value</option>
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198 <option value="pvalue">p-value</option>
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199 </param>
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200 <when value="pvalue">
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201 <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection" help="default: not set (--pvalue)"/>
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202 </when>
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203 <when value="qvalue">
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204 <param name="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. (--qvalue)"/>
0
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205 </when>
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206 </conditional>
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207
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208 <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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209 <option value="peaks_tabular">Peaks as tabular file (compatible wih MultiQC)</option>
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210 <option value="summits">Peak summits</option>
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211 <option value="bdg" >Scores in bedGraph files (--bdg)</option>
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212 <option value="html">Summary page (html)</option>
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213 <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
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214 </param>
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215
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216 <section name="advanced_options" title="Advanced Options">
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217 <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" optional="True"
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218 label="When set, scale the small sample up to the bigger sample"
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219 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. (--to-large). Default: No"/>
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220 <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" optional="True"
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221 label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda). Default: No"/>
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222 <param name="ratio" type="float" optional="True"
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223 label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
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224 help="(--ratio) Default: ignore"/>
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225 <param name="slocal" type="integer" optional="True" label="The small nearby region in basepairs to calculate dynamic lambda"
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226 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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227 <param name="llocal" type="integer" optional="True" label="The large nearby region in basepairs to calculate dynamic lambda"
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228 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. (--llocal) Default: 10000"/>
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229 <conditional name="broad_options">
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230 <param name="broad_options_selector" type="select"
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231 label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff (--broad)">
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232 <option value="nobroad" selected="true">No broad regions</option>
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233 <option value="broad">broad regions</option>
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234 </param>
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235 <when value="broad">
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236 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
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237 help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
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238 </when>
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239 <when value="nobroad">
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240 <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
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241 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"
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242 help="(--call-summits)"/>
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243 </when>
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244 </conditional>
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245 <expand macro="keep_duplicates" />
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246 </section>
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247 </inputs>
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248 <outputs>
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249 <!--callpeaks output-->
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250 <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
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251 <filter> outputs and 'peaks_tabular' in outputs</filter>
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252 </data>
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253 <data name="output_broadpeaks" format="bed" from_work_dir="*_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
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254 <filter>
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255 ((
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256 advanced_options['broad_options']['broad_options_selector'] == "broad"
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257 ))
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258 </filter>
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259 </data>
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260 <data name="output_gappedpeaks" format="bed" from_work_dir="*_peaks.gappedPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
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261 <filter>
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262 ((
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263 advanced_options['broad_options']['broad_options_selector'] == "broad"
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264 ))
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265 </filter>
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266 </data>
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267 <data name="output_narrowpeaks" format="bed" from_work_dir="*_peaks.narrowPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
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268 <filter>
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269 ((
0
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270 advanced_options['broad_options']['broad_options_selector'] == "nobroad"
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271 ))
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272 </filter>
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273 </data>
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274 <data name="output_summits" format="bed" from_work_dir="*_summits.bed" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
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275 <filter>outputs and 'summits' in outputs</filter>
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276 </data>
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277 <data name="output_plot" format="pdf" from_work_dir="*_model.pdf" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (plot)">
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278 <filter>
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279 ((
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280 outputs and 'pdf' in outputs and
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281 nomodel_type['nomodel_type_selector'] == "create_model" and
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282 format != "BAMPE"
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283 ))
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284 </filter>
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285 </data>
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286 <data name="output_treat_pileup" format="bedgraph" from_work_dir="*_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
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287 <filter>outputs and 'bdg' in outputs</filter>
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288 </data>
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289 <data name="output_control_lambda" format="bedgraph" from_work_dir="*_control_lambda.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
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290 <filter>outputs and 'bdg' in outputs</filter>
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291 </data>
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292 <data name="output_extra_files" format="html" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (html report)">
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293 <filter>outputs and 'html' in outputs</filter>
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294 </data>
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295 </outputs>
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296 <tests>
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297 <test expect_num_outputs="5">
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298 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
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299 <param name="c_select" value="Yes"/>
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300 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
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301 <param name="format" value="BED" />
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302 <param name="cutoff_options_selector" value="qvalue"/>
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303 <param name="qvalue" value="0.05"/>
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304 <param name="band_width" value="300"/>
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305 <param name="outputs" value="peaks_tabular,bdg,html"/>
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306 <param name="effective_genome_size_options_selector" value="user_defined" />
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307 <param name="gsize" value="3300000000" />
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308 <param name="lower" value="5" />
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309 <param name="upper" value="50" />
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310 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
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311 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
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312 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/>
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313 <output name="output_extra_files">
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314 <assert_contents>
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315 <has_text text="Additional output created by MACS2" />
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316 </assert_contents>
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317 </output>
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318 </test>
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319 <!-- Ensure pdf can be output -->
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320 <test expect_num_outputs="2">
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321 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
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322 <param name="c_select" value="Yes"/>
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323 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
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324 <param name="format" value="BED" />
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325 <param name="cutoff_options_selector" value="qvalue"/>
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326 <param name="qvalue" value="0.05"/>
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327 <param name="band_width" value="300"/>
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328 <param name="outputs" value="pdf"/>
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329 <param name="effective_genome_size_options_selector" value="user_defined" />
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330 <param name="gsize" value="3300000000" />
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331 <param name="lower" value="5" />
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332 <param name="upper" value="50" />
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333 <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" />
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334 </test>
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335 <!-- Ensure BAMPE works -->
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336 <test expect_num_outputs="1">
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337 <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/>
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338 <param name="format" value="BAMPE" />
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339 <param name="effective_genome_size_options_selector" value="user_defined"/>
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340 <param name="gsize" value="3300000000"/>
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341 <param name="nomodel_type_selector" value="nomodel"/>
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342 <param name="nolambda" value="True"/>
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343 <!-- 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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344 <param name="outputs" value="pdf"/>
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345 <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
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346 </test>
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347 </tests>
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348 <help><![CDATA[
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349
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350 .. class:: infomark
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351
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352 **What it does**
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353
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354 **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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355
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356 -----
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357
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358 **Inputs**
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359
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360 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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361
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362 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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363
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364 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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365
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366 *Effective Genome Size*
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367
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368 PLEASE assign this parameter to fit your needs!
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369
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370 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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371
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372 hs: 2.7e9
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373 mm: 1.87e9
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374 ce: 9e7
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375 dm: 1.2e8
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376
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377 Or see the **deepTools** website for updated information on calculating `Effective Genome Size`_.
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378
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379 -----
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380
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381 **Outputs**
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382
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383 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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384
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385 * **a BED file of peaks** (default)
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386 * a tabular file of peaks (compatible wih MultiQC)
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387 * a BED file of peak summits
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388 * two bedGraph files of scores, for treatment pileup and control lambda
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389 * a HTML summary page
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390 * a PDF plot (if model is built)
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391 * a BED file of broad peaks (if **Composite broad regions** is selected under Advanced Options)
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392 * a BED file of gapped peaks (if **Composite broad regions** is selected under Advanced Options)
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393
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394 **Peaks BED File**
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395
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396 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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397
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398 Example:
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399
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400 ======= ========= ======= ============ ==== === ======= ======== ======= =======
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401 1 2 3 4 5 6 7 8 9 **10**
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402 ======= ========= ======= ============ ==== === ======= ======== ======= =======
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403 chr1 840081 840400 treat1_peak_1 69 . 4.89872 10.50944 6.91052 158
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404 chr1 919419 919785 treat1_peak_2 87 . 5.85158 12.44148 8.70936 130
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405 chr1 937220 937483 treat1_peak_3 66 . 4.87632 10.06728 6.61759 154
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406 ======= ========= ======= ============ ==== === ======= ======== ======= =======
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407
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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408 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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409
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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410 * **1st**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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411 * **2nd**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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412 * **3rd**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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413 * **4th**: name of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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414 * **5th**: integer score for display in genome browser (e.g. UCSC)
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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415 * **6th**: strand, either "." (=no strand) or "+" or "-"
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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416 * **7th**: fold-change
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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417 * **8th**: -log10pvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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418 * **9th**: -log10qvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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419 * **10th**: relative summit position to peak start
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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420
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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421
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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422 **Peaks tabular File**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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423
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c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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424 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**.
8
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425
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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426 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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427
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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428 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
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429 **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)** **fold_enrichment** **-log10(qvalue)** **name**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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430 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
14
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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431 chr1 840082 840400 319 840240 4.00 10.50944 4.89872 6.91052 treat1_peak_1
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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432 chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 treat1_peak_2
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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433 chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 treat1_peak_3
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434 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
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435
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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436 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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437
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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438 * **chr**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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439 * **start**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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440 * **end**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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441 * **length**: length of peak region
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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442 * **abs_summit**: absolute peak summit position
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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443 * **pileup**: pileup height at peak summit
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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444 * **-log10(pvalue)**: -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10)
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445 * **fold_enrichment**: fold enrichment for this peak summit against random Poisson distribution with local lambda
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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446 * **-log10(qvalue)**: -log10(qvalue) at peak summit
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447 * **name**: name of peak
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448
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449 *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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450
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451
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452 **Summits BED File**
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453
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454 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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455
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456 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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457
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458 ======= ========= ======= ============ =======
8
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459 1 2 3 4 **5**
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460 ======= ========= ======= ============ =======
14
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461 chr1 840239 840240 treat1_peak_1 6.91052
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462 chr1 919549 919550 treat1_peak_2 8.70936
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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463 chr1 937374 937375 treat1_peak_3 6.61759
8
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464 ======= ========= ======= ============ =======
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465
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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466 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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467
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468 * **1st**: chromosome name
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469 * **2nd**: start position of peak
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470 * **3rd**: end position of peak
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471 * **4th**: name of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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472 * **5th**: -log10qvalue
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473
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474
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475 **BedGraph Files**
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476
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477 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`_.
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478
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479
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480 Example:
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481
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482 **Treatment pileup file**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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483
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484 ======= ========= ======= =======
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485 1 2 3 **4**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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486 ======= ========= ======= =======
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487 chr1 840146 840147 3.00000
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488 chr1 840147 840332 4.00000
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489 chr1 840332 840335 3.00000
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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490 ======= ========= ======= =======
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491
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492
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493 **Control lambda file**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
494
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
495 ======= ========= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
496 1 2 3 **4**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
497 ======= ========= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
498 chr1 800953 801258 0.02536
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
499 chr1 801258 801631 0.25364
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
500 chr1 801631 801885 0.99858
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
501 ======= ========= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
502
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
503 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
504
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
505 * **1st**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
506 * **2nd**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
507 * **3rd**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
508 * **4th**: treatment pileup score or control local lambda score
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
509
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
510
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
511 **Broad peaks File**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
512
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
513 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.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
514
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
515 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
516
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
517 ======= ========= ======= ============ ==== === ======= ======= =======
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
518 1 2 3 4 5 6 7 8 9
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
519 ======= ========= ======= ============ ==== === ======= ======= =======
14
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 13
diff changeset
520 chr1 840081 840400 treat1_peak_1 52 . 4.08790 8.57605 5.21506
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 13
diff changeset
521 chr1 919419 919785 treat1_peak_2 56 . 4.37270 8.90436 5.60462
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 13
diff changeset
522 chr1 937220 937483 treat1_peak_3 48 . 4.02343 8.06676 4.86861
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
523 ======= ========= ======= ============ ==== === ======= ======= =======
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
524
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
525
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
526 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
527
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
528 * **1st**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
529 * **2nd**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
530 * **3rd**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
531 * **4th**: name of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
532 * **5th**: integer score for display in genome browser (e.g. UCSC)
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
533 * **6th**: strand, either "." (=no strand) or "+" or "-"
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
534 * **7th**: fold-change
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
535 * **8th**: -log10pvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
536 * **9th**: -log10qvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
537
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
538
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
539 **Gapped peaks File**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
540
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
541 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.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
542
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
543 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
544
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
545 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
546 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
547 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
14
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 13
diff changeset
548 chr1 840081 840400 treat1_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 13
diff changeset
549 chr1 919419 919785 treat1_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462
c16dbe4e2db2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 13
diff changeset
550 chr1 937220 937483 treat1_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
551 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
552
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
553 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
554
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
555 * **1st**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
556 * **2nd**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
557 * **3rd**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
558 * **4th**: name of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
559 * **5th**: 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
560 * **6th**: strand, either "." (=no strand) or "+" or "-"
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
561 * **7th**: start of the first narrow peak in the region
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
562 * **8th**: end of the peak
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
563 * **9th**: RGB color key, default colour is 0
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
564 * **10th**: number of blocks, including the starting 1bp and ending 1bp of broad regions
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
565 * **11th**: length of each block, comma-separated values if multiple
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
566 * **12th**: start of each block, comma-separated values if multiple
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
567 * **13th**: fold-change
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
568 * **14th**: -log10pvalue
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
569 * **15th**: -log10qvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
570
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
571 -----
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
572
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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diff changeset
573 **More Information**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
574
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
575 MACS2 performs the following analysis steps:
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
576
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
577 * Artificially extends reads to expected fragment length, and generates coverage map along genome.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
578 * 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.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
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579 * 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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580
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581
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582 **Tips of fine-tuning peak calling**
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583
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584 Check out these other MACS2 tools:
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585
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586 * **MACS2 bdgcmp** can be used on the callpeak bedGraph files or bedGraph files from other resources to calculate score track.
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587 * **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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588 * 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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589
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590 .. class:: warningmark
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591
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592 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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593
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594 .. _MACS2: https://github.com/taoliu/MACS
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595 .. _`Effective Genome Size`: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
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596 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html
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597
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598 @citation@
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599 ]]></help>
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600 <expand macro="citations" />
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601 </tool>