annotate multigps.xml @ 0:4aa531981208 draft

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author iuc
date Mon, 13 Mar 2017 13:25:01 -0400
parents
children 7e0a12282c7f
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iuc
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1 <tool id="multigps" name="MultiGPS" version="0.73.0">
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2 <description>analyzes collections of multi-condition ChIP-seq data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.73">multigps</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 #set output_dir = $output_html.files_path
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12 mkdir -p $output_dir &&
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13 multigps
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iuc
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14 ## General options
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15 ## Append .txt extensions to events hrefs
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16 ## in output dataset so files will render
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17 ## in the browser.
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18 --eventsaretxt
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19 ## Do not run the parallel version of meme
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20 ## since it is not yet available in conda.
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21 --meme1proc
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22 --expt '$expt'
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iuc
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23 --format $expt.ext
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iuc
parents:
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24 #if str($ctrl) != 'None':
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25 --ctrl '$ctrl'
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26 #end if
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27 --threads \${GALAXY_SLOTS:-4}
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28 --geninfo '$chromInfo'
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iuc
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29 ## Advanced options
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iuc
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30 #set aoc = $advanced_options_cond
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31 #if str($aoc.advanced_options) == 'display':
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32 #set bmsc = $aoc.binding_model_smoothing_cond
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33 #set gmsc = $aoc.gauss_model_smoothing_cond
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34 #set rbec = $aoc.report_binding_events_cond
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35 #set rloc = $aoc.reads_limits_options_cond
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36 #set sdc = $aoc.scale_data_cond
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37 #set umc = $aoc.use_motif_cond
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38 #if str($umc.use_motif) == 'yes':
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39 #set rgc = $umc.reference_genome_cond
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40 --seq
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41 #if str($rgc.reference_genome_source) == 'cached':
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42 '${rgc.reference_genome.fields.path}'
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43 #else:
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44 '${rgc.reference_genome}'
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45 #end if
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46 #end if
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47 ## Limits on how many reads
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48 #if str($rloc.reads_limits) == 'yes':
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49 --fixedpb $rloc.fixedpb
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50 --poissongausspb $rloc.poissongausspb
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51 #if str($rloc.nonunique) == 'yes':
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52 --nonunique
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53 #end if
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54 --mappability $rloc.mappability
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55 #if str($rloc.nocache) == 'yes':
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56 --nocache
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57 #end if
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58 #end if
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59 ## Scaling data
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60 #if str($sdc.scale_data) == 'yes':
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61 #if str($sdc.scaling) == 'no':
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62 --noscaling $sdc.scaling
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63 #end if
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64 #if str($sdc.medianscale) == 'yes':
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65 --medianscale $sdc.medianscale
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66 #end if
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67 #if str($sdc.regressionscale) == 'yes':
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68 --regressionscale $sdc.regressionscale
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69 #end if
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70 #if str($sdc.sesscale) == 'yes':
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71 --sesscale $sdc.sesscale
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72 #end if
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73 #if $sdc.fixedscaling > 0:
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74 ‒‒fixedscaling $sdc.fixedscaling
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75 #end if
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76 --scalewin $sdc.scalewin
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77 #if str($sdc.plotscaling) == 'yes':
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78 --plotscaling $sdc.plotscaling
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79 #end if
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80 #end if
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81 ## Running MultiGPS
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82 #if str($aoc.readdistributionfile) != 'None':
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83 --d '$aoc.readdistributionfile'
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84 #end if
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85 --r $aoc.maxtrainingrounds
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86 #if str($aoc.nomodelupdate) == 'no':
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87 --nomodelupdate
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88 #end if
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89 --minmodelupdateevents $aoc.minmodelupdateevents
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90 #if str($bmsc.nomodelsmoothing) == 'no':
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91 --nomodelsmoothing
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92 #else:
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93 --splinesmoothparam $bmsc.splinesmoothparam
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94 #end if
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95 #if str($gmsc.gaussmodelsmoothing) == 'yes':
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96 --gaussmodelsmoothing
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97 --gausssmoothparam $gmsc.gausssmoothparam
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98 #end if
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99 #if str($aoc.jointinmodel) == 'yes':
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100 --jointinmodel
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101 #end if
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102 #if str($aoc.fixedmodelrange) == 'yes':
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103 --fixedmodelrange
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104 #end if
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105 --prlogconf $aoc.prlogconf
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106 #if $aoc.fixedalpha > 0:
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107 --fixedalpha $aoc.fixedalpha
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108 #end if
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109 --alphascale $aoc.alphascale
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110 #if str($aoc.mlconfignotshared) == 'no':
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111 --mlconfignotshared
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112 #end if
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113 #if str($aoc.exclude) != 'None':
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114 --exclude '$aoc.exclude'
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115 #end if
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116 ## MultiGPS priors
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117 #if str($umc.use_motif) == 'yes':
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118 #set mpc = $umc.multigps_priors_cond
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119 #if str($mpc.multigps_priors) == 'yes':
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120 #set bmc = $mpc.both_motifs_cond
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121 #if str($mpc.noposprior) == 'no':
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122 --noposprior
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123 #end if
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124 --probshared $mpc.probshared
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125 #if str($bmc.nomotifs) == 'yes':
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126 --memenmotifs $bmc.memenmotifs
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127 --mememinw $bmc.mememinw
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128 --mememaxw $bmc.mememaxw
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129 #else:
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130 #set mfoc = $bmc.nomotifprior_cond
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131 --nomotifs
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132 --nomotifprior $mfoc.nomotifprior
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133 #if str($mfoc.nomotifprior) == 'yes':
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134 --memenmotifs $mfoc.memenmotifs
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135 --mememinw $mfoc.mememinw
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136 --mememaxw $mfoc.mememaxw
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137 #end if
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138 #end if
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139 #end if
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140 #end if
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141 ## Reporting binding events
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142 #if str($rbec.report_binding_events) == 'yes':
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143 --q $rbec.minqvalue
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iuc
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144 --minfold $rbec.minfold
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iuc
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145 #if str($rbec.nodifftests) == 'no':
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146 --nodifftests
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147 #end if
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iuc
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148 --edgerod $rbec.edgerod
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149 --diffp $rbec.diffp
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150 #end if
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151 #end if
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iuc
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152 2>&1
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iuc
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153 --out '$output_html.files_path'
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iuc
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154 && cp $output_dir/*.events.txt '$experiment_events' || true
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155 && mv $output_dir/*.html '$output_html' || true
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156 && mv $output_dir/*.table.txt '$all_events_table' || true
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157 && mv $output_dir/*.counts '$replicates_counts' || true
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158 ]]>
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159 </command>
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160 <inputs>
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161 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
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162 <validator type="unspecified_build" />
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163 </param>
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164 <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
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165 <!-- Advanced options -->
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166 <conditional name="advanced_options_cond">
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167 <param name="advanced_options" type="select" label="Advanced options">
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168 <option value="hide" selected="true">Hide</option>
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169 <option value="display">Display</option>
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170 </param>
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171 <when value="display">
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172 <!-- Limits on how many reads -->
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173 <conditional name="reads_limits_options_cond">
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174 <param name="reads_limits" type="select" label="Set limits on how many reads can have their 5′ end at the same position in each replicate?" help="Default behavior is to estimate a global per-base limit from a Poisson distribution parameterized by the number of reads divided by the number of mappable bases in the genome. The per-base limit is set as the count corresponding to the 10^-7 probability level from the Poisson.">
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175 <option value="no" selected="True">No</option>
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176 <option value="yes">Yes</option>
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177 </param>
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iuc
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178 <when value="no" />
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179 <when value="yes">
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180 <param name="fixedpb" type="integer" value="0" min="0" label="Fixed per-base limit" help="Zero value estimates from background model"/>
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181 <param name="poissongausspb" type="integer" value="0" min="0" label="Poisson threshold for filtering per base" help="Filter per base using the specified Poisson threshold parameterized by a local Gaussian sliding window" />
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182 <param name="nonunique" type="select" label="Use non-unique reads?">
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183 <option value="no" selected="True">No</option>
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184 <option value="yes">Yes</option>
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185 </param>
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186 <param name="mappability" type="float" value="0.0" min="0.8" label="Fraction of the genome that is mappable for these experiments" />
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iuc
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187 <param name="nocache" type="select" label="Turn off caching of the entire set of experiments?" help="Run slower with less memory" >
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188 <option value="no" selected="True">No</option>
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189 <option value="yes">Yes</option>
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190 </param>
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191 </when>
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192 </conditional>
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iuc
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193 <!-- Scaling data -->
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iuc
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194 <conditional name="scale_data_cond">
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195 <param name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using regression on the set of signal/control ratios in 10Kbp windows.">
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196 <option value="no" selected="True">No</option>
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197 <option value="yes">Yes</option>
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198 </param>
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iuc
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199 <when value="yes">
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200 <param name="scaling" type="select" label="Use signal vs control scaling?">
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iuc
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201 <option value="yes" selected="True">Yes</option>
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iuc
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202 <option value="no">No</option>
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203 </param>
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204 <param name="medianscale" type="select" label="Use the median signal/control ratio as the scaling factor?">
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205 <option value="no" selected="True">No</option>
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206 <option value="yes">Yes</option>
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207 </param>
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iuc
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208 <param name="regressionscale" type="select" label="Use scaling by regression on binned tag counts?">
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iuc
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209 <option value="no" selected="True">No</option>
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iuc
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210 <option value="yes">Yes</option>
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211 </param>
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212 <param name="sesscale" type="select" label="Estimate scaling factor by SES?" help="SES: Diaz, et al. Stat Appl Genet Mol Biol. 2012">
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213 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
214 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
215 </param>
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iuc
parents:
diff changeset
216 <param name="fixedscaling" type="float" value="0.0" min="0.0" label="Multiply control counts by total tag count ratio and then by this factor" help="Set as 0 to skip" />
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iuc
parents:
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217 <param name="scalewin" type="integer" min="0" value="500" label="Window size for estimating scaling ratios" help="The value is the number of base pairs. Use something much smaller than the default if scaling via SES (e.g. 200)." />
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iuc
parents:
diff changeset
218 <param name="plotscaling" type="select" label="Plot diagnostic information for the chosen scaling method?">
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iuc
parents:
diff changeset
219 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
220 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
221 </param>
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iuc
parents:
diff changeset
222 </when>
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iuc
parents:
diff changeset
223 <when value="no" />
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iuc
parents:
diff changeset
224 </conditional>
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iuc
parents:
diff changeset
225 <!-- Running MultiGPS -->
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iuc
parents:
diff changeset
226 <param name="readdistributionfile" type="data" optional="True" format="tabular" label="Optional binding event read distribution file for initializing models" help="A default initial distribution appropriate for ChIP-seq data is used if this option is not specified." />
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iuc
parents:
diff changeset
227 <param name="maxtrainingrounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" />
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iuc
parents:
diff changeset
228 <param name="nomodelupdate" type="select" label="Perform binding model updates?">
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iuc
parents:
diff changeset
229 <option value="yes" selected="True">Yes</option>
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iuc
parents:
diff changeset
230 <option value="no">No</option>
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iuc
parents:
diff changeset
231 </param>
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iuc
parents:
diff changeset
232 <param name="minmodelupdateevents" type="integer" value="500" min="0" label="Minimum number of events to support an update of the read distribution" />
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iuc
parents:
diff changeset
233 <conditional name="binding_model_smoothing_cond">
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iuc
parents:
diff changeset
234 <param name="nomodelsmoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline.">
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iuc
parents:
diff changeset
235 <option value="yes" selected="True">Yes</option>
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iuc
parents:
diff changeset
236 <option value="no">No</option>
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iuc
parents:
diff changeset
237 </param>
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iuc
parents:
diff changeset
238 <when value="yes">
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iuc
parents:
diff changeset
239 <param name="splinesmoothparam" type="integer" value="30" min="0" label="Spline smoothing parameter" />
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iuc
parents:
diff changeset
240 </when>
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iuc
parents:
diff changeset
241 <when value="no" />
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iuc
parents:
diff changeset
242 </conditional>
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iuc
parents:
diff changeset
243 <conditional name="gauss_model_smoothing_cond">
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iuc
parents:
diff changeset
244 <param name="gaussmodelsmoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline.">
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iuc
parents:
diff changeset
245 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
246 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
247 </param>
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iuc
parents:
diff changeset
248 <when value="no" />
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iuc
parents:
diff changeset
249 <when value="yes">
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iuc
parents:
diff changeset
250 <param name="gausssmoothparam" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
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iuc
parents:
diff changeset
251 </when>
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iuc
parents:
diff changeset
252 </conditional>
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iuc
parents:
diff changeset
253 <param name="jointinmodel" type="select" label="Allow joint events in model updates?">
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iuc
parents:
diff changeset
254 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
255 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
256 </param>
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iuc
parents:
diff changeset
257 <param name="fixedmodelrange" type="select" label="Keep binding model range fixed to inital size?" help="Select No to vary automatically">
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iuc
parents:
diff changeset
258 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
259 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
260 </param>
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iuc
parents:
diff changeset
261 <param name="prlogconf" type="integer" value="-6" label="Poisson log threshold for potential region scanning" />
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iuc
parents:
diff changeset
262 <param name="fixedalpha" type="integer" value="0" min="0" label="Impose this alpha" help="This is a sparse prior on binding events in the MultiGPS model. It can be interpreted as a minimum number of reads that each binding event must be responsible for in the model. A zero value will estimate the alpha automatically." />
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iuc
parents:
diff changeset
263 <param name="alphascale" type="float" value="1.0" min="0" label="Alpha scaling factor" />
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iuc
parents:
diff changeset
264 <param name="mlconfignotshared" type="select" label="Share component configs in the ML step?" help="Mainly affects the quantification of binding levels for binding events that are not shared but are located at nearby locations across experiments.">
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iuc
parents:
diff changeset
265 <option value="yes" selected="True">Yes</option>
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iuc
parents:
diff changeset
266 <option value="no">No</option>
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iuc
parents:
diff changeset
267 </param>
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iuc
parents:
diff changeset
268 <param name="exclude" type="data" optional="True" format="txt" label="Optional file containing a set of regions to ignore during MultiGPS training" help="Ideally exclude the mitochondrial genome and other blacklisted regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments." />
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iuc
parents:
diff changeset
269 <!-- MultiGPS priors -->
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iuc
parents:
diff changeset
270 <conditional name="use_motif_cond">
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iuc
parents:
diff changeset
271 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
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iuc
parents:
diff changeset
272 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
273 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
274 </param>
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iuc
parents:
diff changeset
275 <when value="yes">
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iuc
parents:
diff changeset
276 <!-- Specifying the genome -->
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iuc
parents:
diff changeset
277 <conditional name="reference_genome_cond">
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iuc
parents:
diff changeset
278 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
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iuc
parents:
diff changeset
279 <option value="cached">locally cached</option>
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iuc
parents:
diff changeset
280 <option value="history">from history</option>
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iuc
parents:
diff changeset
281 </param>
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iuc
parents:
diff changeset
282 <when value="cached">
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iuc
parents:
diff changeset
283 <param name="reference_genome" type="select" label="Using reference genome">
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iuc
parents:
diff changeset
284 <options from_data_table="all_fasta">
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iuc
parents:
diff changeset
285 <filter type="data_meta" key="dbkey" ref="expt" column="1"/>
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iuc
parents:
diff changeset
286 </options>
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iuc
parents:
diff changeset
287 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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iuc
parents:
diff changeset
288 </param>
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iuc
parents:
diff changeset
289 </when>
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iuc
parents:
diff changeset
290 <when value="history">
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iuc
parents:
diff changeset
291 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
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iuc
parents:
diff changeset
292 <options>
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iuc
parents:
diff changeset
293 <filter type="data_meta" key="dbkey" ref="expt"/>
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iuc
parents:
diff changeset
294 </options>
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iuc
parents:
diff changeset
295 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
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iuc
parents:
diff changeset
296 </param>
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iuc
parents:
diff changeset
297 </when>
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iuc
parents:
diff changeset
298 </conditional>
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iuc
parents:
diff changeset
299 <!-- MultiGPS priors options -->
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iuc
parents:
diff changeset
300 <conditional name="multigps_priors_cond">
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iuc
parents:
diff changeset
301 <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?">
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iuc
parents:
diff changeset
302 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
303 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
304 </param>
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iuc
parents:
diff changeset
305 <when value="no" />
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iuc
parents:
diff changeset
306 <when value="yes">
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iuc
parents:
diff changeset
307 <param name="noposprior" type="select" label="Perform inter-experiment positional prior?">
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iuc
parents:
diff changeset
308 <option value="yes" selected="True">Yes</option>
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iuc
parents:
diff changeset
309 <option value="no">No</option>
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iuc
parents:
diff changeset
310 </param>
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iuc
parents:
diff changeset
311 <param name="probshared" type="float" value="0.9" min="0.0" label="Probability that events are shared across conditions" />
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iuc
parents:
diff changeset
312 <conditional name="both_motifs_cond">
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iuc
parents:
diff changeset
313 <param name="nomotifs" type="select" label="Perform both motif-finding and motif priors?">
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iuc
parents:
diff changeset
314 <option value="yes" selected="True">Yes</option>
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iuc
parents:
diff changeset
315 <option value="no">No</option>
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iuc
parents:
diff changeset
316 </param>
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iuc
parents:
diff changeset
317 <when value="yes">
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iuc
parents:
diff changeset
318 <expand macro="motif_finding_params" />
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iuc
parents:
diff changeset
319 </when>
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iuc
parents:
diff changeset
320 <when value="no">
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iuc
parents:
diff changeset
321 <conditional name="nomotifprior_cond">
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iuc
parents:
diff changeset
322 <param name="nomotifprior" type="select" label="Perform motif-finding only?" help="Selecting Yes turns off motif priors.">
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iuc
parents:
diff changeset
323 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
324 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
325 </param>
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iuc
parents:
diff changeset
326 <when value="no" />
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iuc
parents:
diff changeset
327 <when value="yes">
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iuc
parents:
diff changeset
328 <expand macro="motif_finding_params" />
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iuc
parents:
diff changeset
329 </when>
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iuc
parents:
diff changeset
330 </conditional>
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iuc
parents:
diff changeset
331 </when>
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iuc
parents:
diff changeset
332 </conditional>
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iuc
parents:
diff changeset
333 </when>
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iuc
parents:
diff changeset
334 </conditional>
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iuc
parents:
diff changeset
335 </when>
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iuc
parents:
diff changeset
336 <when value="no" />
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iuc
parents:
diff changeset
337 </conditional>
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iuc
parents:
diff changeset
338 <!-- Reporting binding events -->
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iuc
parents:
diff changeset
339 <conditional name="report_binding_events_cond">
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iuc
parents:
diff changeset
340 <param name="report_binding_events" type="select" label="Report binding events?">
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iuc
parents:
diff changeset
341 <option value="no" selected="True">No</option>
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iuc
parents:
diff changeset
342 <option value="yes">Yes</option>
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iuc
parents:
diff changeset
343 </param>
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iuc
parents:
diff changeset
344 <when value="no" />
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iuc
parents:
diff changeset
345 <when value="yes">
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iuc
parents:
diff changeset
346 <param name="minqvalue" type="float" min="0" value="0.001" label="Minimum Q-value (corrected p-value) of reported binding events" />
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iuc
parents:
diff changeset
347 <param name="minfold" type="float" min="0" value="1.5" label="Minimum event fold-change vs scaled control" />
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iuc
parents:
diff changeset
348 <param name="nodifftests" type="select" label="Run differential enrichment tests?">
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iuc
parents:
diff changeset
349 <option value="yes" selected="True">Yes</option>
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iuc
parents:
diff changeset
350 <option value="no">No</option>
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iuc
parents:
diff changeset
351 </param>
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iuc
parents:
diff changeset
352 <param name="edgerod" type="float" min="0" value="0.15" label="EdgeR over-dispersion parameter value" />
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iuc
parents:
diff changeset
353 <param name="diffp" type="float" min="0" value="0.01" label="Minimum p-value for reporting differential enrichment" />
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iuc
parents:
diff changeset
354 </when>
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iuc
parents:
diff changeset
355 </conditional>
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iuc
parents:
diff changeset
356 </when>
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iuc
parents:
diff changeset
357 <when value="hide" />
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iuc
parents:
diff changeset
358 </conditional>
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iuc
parents:
diff changeset
359 </inputs>
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iuc
parents:
diff changeset
360 <outputs>
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iuc
parents:
diff changeset
361 <data name="replicates_counts" format="tabular" label="${tool.name} replicates counts on ${on_string}"/>
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iuc
parents:
diff changeset
362 <data name="all_events_table" format="tabular" label="${tool.name} all events table on ${on_string}"/>
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iuc
parents:
diff changeset
363 <data name="experiment_events" format="tabular" label="${tool.name} experiment events on ${on_string}"/>
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iuc
parents:
diff changeset
364 <data name="output_html" format="html" label="${tool.name} on ${on_string}"/>
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iuc
parents:
diff changeset
365 </outputs>
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iuc
parents:
diff changeset
366 <tests>
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iuc
parents:
diff changeset
367 <test>
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iuc
parents:
diff changeset
368 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
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iuc
parents:
diff changeset
369 <param name="advanced_options_cond" value="hide" />
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iuc
parents:
diff changeset
370 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
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iuc
parents:
diff changeset
371 <output name="experiment_events" file="hg19_experiment_events1.tabular" ftype="tabular"/>
4aa531981208 Uploaded
iuc
parents:
diff changeset
372 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
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iuc
parents:
diff changeset
373 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
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iuc
parents:
diff changeset
374 </test>
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iuc
parents:
diff changeset
375 <test>
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iuc
parents:
diff changeset
376 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
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iuc
parents:
diff changeset
377 <param name="ctrl" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
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iuc
parents:
diff changeset
378 <param name="advanced_options_cond" value="display" />
4aa531981208 Uploaded
iuc
parents:
diff changeset
379 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
4aa531981208 Uploaded
iuc
parents:
diff changeset
380 <output name="experiment_events" file="hg19_experiment_events2.tabular" ftype="tabular"/>
4aa531981208 Uploaded
iuc
parents:
diff changeset
381 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
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iuc
parents:
diff changeset
382 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
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iuc
parents:
diff changeset
383 </test>
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iuc
parents:
diff changeset
384 </tests>
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iuc
parents:
diff changeset
385 <help>
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iuc
parents:
diff changeset
386
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iuc
parents:
diff changeset
387 **What it does**
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iuc
parents:
diff changeset
388
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iuc
parents:
diff changeset
389 MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing
4aa531981208 Uploaded
iuc
parents:
diff changeset
390 differential binding events between conditions. MultiGPS encourages consistency in the reported binding
4aa531981208 Uploaded
iuc
parents:
diff changeset
391 event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event.
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iuc
parents:
diff changeset
392 MultiGPS performs significant EM optimization of binding events along the genome and across experimental
4aa531981208 Uploaded
iuc
parents:
diff changeset
393 conditions, and it integrates motif-finding via MEME. The tool loads all data into memory, so the potential
4aa531981208 Uploaded
iuc
parents:
diff changeset
394 exists for time and memory intensive analyses if running over many conditions or large datasets.
4aa531981208 Uploaded
iuc
parents:
diff changeset
395
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iuc
parents:
diff changeset
396 -----
4aa531981208 Uploaded
iuc
parents:
diff changeset
397
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iuc
parents:
diff changeset
398 **Options**
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iuc
parents:
diff changeset
399
4aa531981208 Uploaded
iuc
parents:
diff changeset
400 * **Loading data:**
4aa531981208 Uploaded
iuc
parents:
diff changeset
401
4aa531981208 Uploaded
iuc
parents:
diff changeset
402 - **Optional file containing reads from a control experiment** - must be same format as input experiment
4aa531981208 Uploaded
iuc
parents:
diff changeset
403 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
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iuc
parents:
diff changeset
404 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
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iuc
parents:
diff changeset
405 - **Use non-unique reads** - Use non-unique reads.
4aa531981208 Uploaded
iuc
parents:
diff changeset
406 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments
4aa531981208 Uploaded
iuc
parents:
diff changeset
407 - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory).
4aa531981208 Uploaded
iuc
parents:
diff changeset
408
4aa531981208 Uploaded
iuc
parents:
diff changeset
409 * **Scaling control vs signal counts:**
4aa531981208 Uploaded
iuc
parents:
diff changeset
410
4aa531981208 Uploaded
iuc
parents:
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411 - **Use signal vs control scaling?** - Flag to turn off auto estimation of signal vs control scaling factor
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412 - **Use the median signal/control ratio as the scaling factor?** - Flag to use scaling by median ratio (default = scaling by NCIS).
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413 - **Use scaling by regression on binned tag counts?** - Flag to use scaling by regression (default = scaling by NCIS).
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414 - **Estimate scaling factor by SES?** - Specify whether to estimate scaling factor by SES.
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415 - **Multiply control counts by total tag count ratio and then by this factor** - Multiply control counts by total tag count ratio and then by this factor (default: NCIS).
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416 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios
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417 - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method.
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418
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419 * **Running MultiGPS:**
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420
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421 - **Optional binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
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422 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions.
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423 - **Perform binding model updates?** - Perform binding model updates?
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424 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution
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425 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor.
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426 - **Spline smoothing parameter** - Smoothing parameter for smoothing cubic spline.
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427 - **Perform Gaussian model smoothing?** - Select "Yes" to use Gaussian model smoothing using a specified smoothing factor if binding model smoothing is not performed.
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428 - **Allow joint events in model updates?** - Specify whether to allow joint events in model updates.
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429 - **Keep binding model range fixed to inital size?** - Flag to keep binding model range fixed to inital size (default: vary automatically)
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430 - **Poisson log threshold for potential region scanning** - Poisson log threshold for potential region scanning.
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431 - **Alpha scaling factor** - Alpha scaling factor. Increasing this parameter results in stricter binding event calls.
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432 - **Impose this alpha** - The alpha parameter is a sparse prior on binding events in the MultiGPS model. It can be interpreted as a minimum number of reads that each binding event must be responsible for in the model. Default: estimate alpha automatically.
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433 - **Share component configs in the ML step?** - Flag to not share component configs in the ML step
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434 - **Optional file containing a set of regions to ignore during MultiGPS training** - File containing a set of regions to ignore during MultiGPS training. It’s a good idea to exclude the mitochondrial genome and other ‘blacklisted’ regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments. MultiGPS will waste time trying to model binding events in these regions, even though they will not typically appear significantly enriched over the control (and thus will not be reported to the user).
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435
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436 * **MultiGPS priors:**
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437
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438 - **Perform inter-experiment positional prior?** - Flag to turn off inter-experiment positional prior (default=on).
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439 - **Probability that events are shared across conditions** - Probability that events are shared across conditions.
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440 - **Perform both motif-finding and motif priors?** - Flag to turn off motif-finding and motif priors.
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441 - **Perform motif-finding only?** - Flag to turn off motif priors only.
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442 - **Number of motifs MEME should find for each condition** - Number of motifs MEME should find for each condition.
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443 - **Minimum motif width for MEME** - minw arg for MEME.
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444 - **Maximum motif width for MEME** - maxw arg for MEME.
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445
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446 * **Reporting binding events:**
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447
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448 - **Minimum Q-value (corrected p-value) of reported binding events** - Minimum Q-value (corrected p-value) of reported binding events.
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449 - **Minimum event fold-change vs scaled control** - Minimum event fold-change vs scaled control.
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450 - **Run differential enrichment tests?** - Choose whether to run differential enrichment tests.
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451 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
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452 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.
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453
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454 </help>
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455 <citations>
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456 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
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457 </citations>
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458 </tool>