annotate bamCorrelate.xml @ 31:7889d260cc37 draft default tip

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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date Wed, 21 Oct 2015 02:50:24 -0400
parents 5231f398d784
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1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="@WRAPPER_VERSION@.0">
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2 <description>correlates pairs of BAM files</description>
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3 <macros>
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4 <token name="@BINARY@">bamCorrelate</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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10 #set files=[]
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11 #set labels=[]
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12
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13 @multiple_input_bams@
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14
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15 bamCorrelate
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16
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17 $mode.modeOpt
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18
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19 @THREADS@
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20
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21 --bamfiles '#echo "' '".join($files)#'
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22 --labels '#echo "' '".join($labels)#'
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23 --fragmentLength $fragmentLength
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24 --corMethod $corMethod
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25
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26 --plotFile $outFileName
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27
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28 #if $output.showOutputSettings == "yes"
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29 --outRawCounts '$outFileRawCounts'
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30 --outFileCorMatrix '$outFileCorMatrix'
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31 --plotFileFormat '$output.outFileFormat'
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32 #else:
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33 --plotFileFormat 'png'
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34 #end if
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35
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36 #if $mode.modeOpt == "bins":
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37 --binSize '$mode.binSize'
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38 --distanceBetweenBins '$mode.distanceBetweenBins'
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39 $mode.doNotRemoveOutliers
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40 #else:
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41 --BED $mode.region_file
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42 #end if
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43
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44 #### options available in both modes
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45 #if str($mode.region.value) != '':
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46 --region '$mode.region'
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47 #end if
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48
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49 #if $plotTitle and str($plotTitle).strip() != "":
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50 --plotTitle '$plotTitle'
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51 #end if
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52 $plotNumbers
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53 #if $mode.advancedOpt.showAdvancedOpt == "yes":
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54
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55 $mode.advancedOpt.doNotExtendPairedEnds
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56 $mode.advancedOpt.ignoreDuplicates
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57 $mode.advancedOpt.includeZeros
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58
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59 #if $mode.advancedOpt.minMappingQuality:
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60 --minMappingQuality '$mode.advancedOpt.minMappingQuality'
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61 #end if
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62
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63 #if $mode.advancedOpt.zMin:
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64 --zMin $mode.advancedOpt.zMin
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65 #end if
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66 #if $mode.advancedOpt.zMax:
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67 --zMax $mode.advancedOpt.zMax
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68 #end if
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69 --colorMap '$mode.advancedOpt.colorMap'
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70
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71 #end if
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72 ]]>
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73 </command>
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74
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75 <inputs>
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76 <expand macro="multiple_input_bams" />
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77
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78 <param name="fragmentLength" type="integer" value="200" min="1"
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79 label="Length of the average fragment size"
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80 help ="Reads will be extended to match this length unless they are paired-end,
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81 in which case they will be extended to match the fragment length.
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82 *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will
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83 be extended to match the fragment length. (--fragmentLength)"/>
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84
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85 <param name="corMethod" type="select" label="Correlation method">
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86 <option value="spearman" selected="True">Spearman</option>
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87 <option value="pearson">Pearson</option>
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88 </param>
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89
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90 <conditional name="mode">
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91 <param name="modeOpt" type="select" label="Choose computation mode"
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92 help="In the bins mode, the correlation is computed based on equal
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93 length bins. In the BED file mode, as list of genomic regions in BED
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94 format has to be given. For each region in the BED file the number of
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95 overlapping reads is counted in each of the BAM files.
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96 Then the correlation is computed.">
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97 <option value="bins" selected="true">Bins</option>
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98 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
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99 </param>
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100 <when value="bins">
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101 <param name="binSize" type="integer" value="10000" min="1"
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102 label="Bin size in bp"
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103 help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
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104
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105 <param name="distanceBetweenBins" type="integer" value="0" min="0"
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106 label="Distance between bins"
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107 help="By default, bamCorrelate considers consecutive bins of
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108 the specified 'Bin size'. However, to reduce the
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109 computation time, a larger distance between bins can
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110 by given. Larger distances result in less bins being
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111 considered. (--distanceBetweenBins)"/>
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112
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113 <param name="doNotRemoveOutliers" type="boolean"
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114 truevalue="--doNotRemoveOutliers" falsevalue="" label="Do not filter outliers"
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115 help="By default, bins with very large counts are removed.
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116 By setting this option, outliers will not be
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117 removed. Bins with unusually large counts normally
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118 correspond to regions in the genome that accumulate
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119 lot of reads like satellite regions. If outliers are not
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120 removed the pearson correlation will wrongly report a
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121 very high correlation; that's why, by default,
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122 bamCorrelate tries to remove outliers using
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123 the median absolute deviation (MAD) method applying a
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124 threshold of 200 to only consider extremely large
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125 deviations from the median. (--doNotRemoveOutliers)"/>
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126
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127 <expand macro="bamCorrelate_mode_actions" />
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128 </when>
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129 <when value="BED-file">
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130 <param name="region_file" type="data" format="bed"
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131 label="Region file in BED format"
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132 help="Correlation is computed for the number of reads that overlap such regions."/>
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133 <expand macro="bamCorrelate_mode_actions" />
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134 </when>
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135 </conditional>
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136 <expand macro="plotTitle" />
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137 <expand macro="plotNumbers" />
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138 <conditional name="output">
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139 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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140 <option value="no" selected="true">no</option>
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141 <option value="yes">yes</option>
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142 </param>
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143 <when value="no" />
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144 <when value="yes">
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145 <expand macro="input_image_file_format"/>
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146 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
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147 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
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148 </when>
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149 </conditional>
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150
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151 </inputs>
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152 <outputs>
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153 <expand macro="output_image_file_format" />
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154 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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155 <filter>
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156 ((
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157 output['showOutputSettings'] == 'yes' and
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158 output['saveRawCounts'] is True
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159 ))
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160 </filter>
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161 </data>
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162 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
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163 <filter>
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164 ((
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165 output['showOutputSettings'] == 'yes' and
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166 output['saveCorMatrix'] is True
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167 ))
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168 </filter>
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169 </data>
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170 </outputs>
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171 <tests>
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172 <test>
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173 <repeat name="input_files">
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174 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
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175 <param name="label" value="first BAM file" />
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176 </repeat>
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177 <repeat name="input_files">
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178 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
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179 <param name="label" value="second BAM file" />
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180 </repeat>
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181 <param name="modeOpt" value="bins" />
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182 <param name="binSize" value="10" />
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183 <param name="showOutputSettings" value="no" />
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184 <output name="outFileName" file="bamCorrelate_result1.png" ftype="png" compare="sim_size" />
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185 </test>
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186 </tests>
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187 <help>
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188 <![CDATA[
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189 **What it does**
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190
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191 This tool is useful to assess the overall similarity of different BAM files. A typical application
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192 is to check the correlation between replicates or published data sets.
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193
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194 The tool splits the genomes into bins of given length. For each bin, the number of reads
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195 found in each BAM file is counted and a correlation (either Pearson or Spearman) is computed for all
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196 pairs of BAM files. Finally, a heatmap is drawn based on the similarity of the samples.
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197
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198
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199 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
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200 :alt: Heatmap of RNA Polymerase II ChIP-seq
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201
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202
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203 You can find more details on the bamCorrelate wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamCorrelate
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204
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205
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206 **Output files**:
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207
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208 - **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example
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209 - data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used
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210
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211
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212 -----
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213
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214 @REFERENCES@
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215 ]]>
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216 </help>
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217 <expand macro="citations" />
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218 </tool>