Mercurial > repos > bgruening > deeptools_multi_bigwig_summary

annotate deepTools_macros.xml.orig @ 7:77276bcad67f draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author bgruening
date Wed, 09 Mar 2016 17:17:35 -0500
parents 263b4adf3520
children
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1 <macros>
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2
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3 <xml name="advancedOpt_scaffold">
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4 <conditional name="advancedOpt">
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5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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6 <option value="no" selected="true">no</option>
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7 <option value="yes">yes</option>
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8 </param>
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9 <when value="no" />
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10 <when value="yes">
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11 <yield/>
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12 </when>
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13 </conditional>
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14 </xml>
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15
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16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
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17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
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18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
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19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
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20 --extendReads
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21 #end if
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22 $advancedOpt.ignoreDuplicates
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23 $advancedOpt.centerReads
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24 #if $advancedOpt.minMappingQuality:
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25 --minMappingQuality '$advancedOpt.minMappingQuality'
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26 #end if
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27 #if $advancedOpt.samFlagInclude:
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28 --samFlagInclude $advancedOpt.samFlagInclude
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29 #end if
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30 #if $advancedOpt.samFlagExclude:
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31 --samFlagExclude $advancedOpt.samFlagExclude
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32 #end if
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33 </token>
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34
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35 <xml name="heatmap_options">
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36 <expand macro="zMin_zMax" />
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37 <expand macro="colorMap" />
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38 <expand macro="plotTitle" />
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39 <expand macro="plotNumbers" />
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40 </xml>
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41
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42 <token name="@HEATMAP_OPTIONS@">
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43 #if str($plotting_type.zMin) != "":
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44 --zMin $plotting_type.zMin
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45 #end if
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46 #if str($plotting_type.zMax) != "":
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47 --zMax $plotting_type.zMax
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48 #end if
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49 --colorMap '$plotting_type.colorMap'
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50 $plotting_type.plotNumbers
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51 --plotTitle '$plotting_type.plotTitle'
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52 </token>
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53
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54
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55 <xml name="includeZeros">
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56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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57 label="Include zeros"
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58 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
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59 </xml>
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60
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61 <xml name="zMin_zMax">
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62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
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63 help="If not specified the value is set automatically."/>
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64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
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65 help="If not specified the value is set automatically."/>
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66 </xml>
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67
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68 <xml name="region_limit_operation">
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69 <param argument="--region" type="text" value=""
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70 label="Region of the genome to limit the operation to"
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71 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
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72 </xml>
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73
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74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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75 <<<<<<< HEAD
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76 <token name="@WRAPPER_VERSION@">2.0.1.0</token>
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77 =======
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78 <token name="@WRAPPER_VERSION@">2.1.0</token>
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79 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
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80 <xml name="requirements">
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81 <requirements>
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82 <requirement type="package" version="2.7.10">python</requirement>
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83 <requirement type="binary">@BINARY@</requirement>
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84 <<<<<<< HEAD
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85 <requirement type="package" version="2.0.1">deepTools</requirement>
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86 =======
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87 <requirement type="package" version="2.1.0">deepTools</requirement>
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88 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
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89 <yield />
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90 </requirements>
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91 <expand macro="stdio" />
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92 <version_command>@BINARY@ --version</version_command>
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93 </xml>
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94
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95 <xml name="smoothLength">
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96 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
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97 label="Smooth values using the following length (in bases)"
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98 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
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99 </xml>
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100
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101
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102 <xml name="kmeans_clustering">
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103 <conditional name="used_multiple_regions">
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104 <param name="used_multiple_regions_options" type="select"
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105 label="Did you compute the matrix with more than one groups of regions?"
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106 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
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107 <option value="yes">Yes, I used multiple groups of regions</option>
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108 <option value="no">No, I used only one group</option>
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109 </param>
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110 <when value="no">
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111 <conditional name="clustering">
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112 <param name="clustering_options" type="select" label="Clustering algorithm">
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113 <option value="none">No clustering</option>
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114 <option value="kmeans">Kmeans clustering</option>
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115 <option value="hclust">Hierarchical clustering</option>
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116 </param>
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117 <when value="kmeans">
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118 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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119 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
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120 This only works for data that is not grouped, otherwise only the first group will be clustered.
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121 If more specific clustering methods are required it is advisable to save the underlying matrix and
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122 run the clustering using other software."/>
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123 </when>
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124 <when value="hclust">
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125 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
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126 help="WARNING: This option causes the tool to run for a very long time! When this option is
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127 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
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128 This only works for data that is not grouped, otherwise only the first group will be clustered.
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129 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
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130 If more specific clustering methods are required it is advisable to save the underlying matrix and
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131 run the clustering using other software."/>
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132 </when>
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133 <when value="none" />
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134 </conditional>
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135 </when>
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136 <when value="yes" />
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137 </conditional>
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138 </xml>
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139
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140 <token name="@KMEANS_CLUSTERING@">
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141 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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142 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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143 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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144 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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145 #end if
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146 #end if
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147 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
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148 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
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149 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
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150 #end if
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151 #end if
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152 #end if
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153 </token>
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154
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155 <xml name="samFlags">
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156 <param argument="--samFlagInclude" type="integer" optional="True" value=""
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157 label="Include reads based on the SAM flag"
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158 help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
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159 <param argument="--samFlagExclude" type="integer" optional="True" value=""
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160 label="Exclude reads based on the SAM flag"
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161 help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
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162 </xml>
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163
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164 <xml name="read_processing_options">
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165 <expand macro="extendReads" />
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166 <expand macro="ignoreDuplicates" />
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167 <expand macro="centerReads" />
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168 <expand macro="minMappingQuality" />
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169 <expand macro="samFlags" />
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170 </xml>
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171
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172 <xml name="plotNumbers">
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173 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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174 label="Plot the correlation value"
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175 help="If set, then the correlation number is plotted on top of the heatmap."/>
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176 </xml>
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177
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178 <xml name="extendReads">
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179 <conditional name="doExtendCustom">
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180 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
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181 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
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182 By default *each* read mate is extended.
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183 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
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184 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
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185 Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
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186 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
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187 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
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188 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
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189 <option value="custom">A custom length, which will be applied to ALL reads.</option>
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190 </param>
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191 <when value="no" />
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192 <when value="yes" />
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193 <when value="custom">
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194 <param name="extendReadsValue" type="integer" value="300" min="1"
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195 label="Extend reads to the given average fragment size"
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196 help="Extend all reads to this length" />
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197 </when>
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198 </conditional>
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199 </xml>
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200
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201 <xml name="corMethod">
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202 <param argument="--corMethod" type="select" label="Correlation method">
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203 <option value="spearman" selected="True">Spearman</option>
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204 <option value="pearson">Pearson</option>
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205 </param>
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206 </xml>
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207
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208 <xml name="distanceBetweenBins">
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209 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
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210 label="Distance between bins"
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211 help="By default, multiBamSummary considers consecutive bins of
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212 the specified 'Bin size'. However, to reduce the
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213 computation time, a larger distance between bins can
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214 be given. Larger distances result in fewer bins being
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215 considered."/>
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216 </xml>
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217
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218 <xml name="centerReads">
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219 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
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220 label="Center regions with respect to the fragment length"
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221 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
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222 </xml>
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223
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224 <xml name="ignoreDuplicates">
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225 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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226 label="Ignore duplicates"
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227 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
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228 </xml>
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229
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230 <xml name="sortUsing">
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231 <param argument="--sortUsing" type="select" label="Method used for sorting"
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232 help="For each row the method is computed.">
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233 <option value="mean" selected="true">mean</option>
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234 <option value="median">median</option>
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235 <option value="min">min</option>
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236 <option value="max">max</option>
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237 <option value="sum">sum</option>
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238 <option value="region_length">region length</option>
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239 </param>
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240 </xml>
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241
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242 <xml name="sortRegions">
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243 <param argument="--sortRegions" type="select" label="Sort regions"
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244 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
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245 <option value="no">no ordering</option>
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246 <option value="descend" selected="true">descending order</option>
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247 <option value="ascend">ascending order</option>
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248 </param>
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249 </xml>
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250
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251 <xml name="minMappingQuality">
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252 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
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253 label="Minimum mapping quality"
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254 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
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255 </xml>
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256
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257 <xml name="skipZeros">
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258 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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259 label ="Skip zeros"
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260 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />
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261 </xml>
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262
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263 <xml name="fragmentLength">
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264 <param argument="--fragmentLength" type="integer" value="300" min="1"
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265 label="Fragment length used for the sequencing"
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266 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
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267 </xml>
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268
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269 <xml name="scaleFactor">
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270 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
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271 help="When used in combination with --normalizeTo1x or
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272 --normalizeUsingRPKM, the computed scaling factor will
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273 be multiplied by the given scale factor." />
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274 </xml>
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275
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276 <xml name="scaleFactors">
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277 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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278 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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279 </xml>
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280
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281 <xml name="stdio">
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282 <stdio>
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283 <exit_code range="1:" />
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284 <exit_code range=":-1" />
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285 <regex match="Error:" />
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286 <regex match="Exception:" />
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287 <regex match="EXception:" />
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288 <regex match="Traceback" />
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289 </stdio>
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290 </xml>
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291
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292 <xml name="pseudocount">
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293 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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294 </xml>
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295
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296 <token name="@REFERENCES@">
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297
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298 .. class:: infomark
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299
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300 For more information on the tools, please visit our `help site`_.
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301
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302 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
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303
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304 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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305
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306 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
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307 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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308 .. _help site: https://deeptools.readthedocs.org/
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309
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310 </token>
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311 <xml name="citations">
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312 <citations>
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313 <citation type="doi">10.1093/nar/gku365</citation>
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314 <yield />
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315 </citations>
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316 </xml>
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317
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318 <xml name="multiple_input_bams">
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319 <param argument="--bamfiles" type="data" format="bam" min="2"
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320 label="Bam file" multiple="true"
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321 help="The BAM file must be sorted."/>
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322 </xml>
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323
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324 <xml name="multiple_input_bigwigs">
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325 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
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326 label="Bigwig file"
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327 help="A Bigwig file."/>
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328 </xml>
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329
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330 <xml name="plotTitle">
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331 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
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332 label="Title of the plot"
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333 help="Title of the plot, to be printed on top of the generated image." />
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334 </xml>
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335
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336
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337 <token name="@multiple_input_bams@">
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338 <![CDATA[
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339 #set files=[]
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340 #set labels=[]
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341 #for $counter, $bamfile in enumerate($bamfiles):
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342 ln -s "${bamfile}" "./${counter}.bam" &&
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343 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
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344 #silent $files.append('%s.bam' % $counter)
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345 #silent $labels.append('%s' % ($bamfile.display_name))
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346 #end for
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347 ]]>
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348 </token>
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349
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350 <token name="@multiple_input_bigwigs@">
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351 <![CDATA[
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352 #set files=[]
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353 #set labels=[]
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354 #for $counter, $bigwig in enumerate($bigwigfiles):
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355 ln -s "${bigwig}" "${counter}.bw" &&
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356 #silent $files.append('%s.bw' % $counter)
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357 #silent $labels.append('%s' % ($bigwig.display_name))
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358 #end for
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359 ]]>
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360 </token>
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361
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362 <xml name="reference_genome_source">
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363 <conditional name="source">
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364 <param name="ref_source" type="select" label="Reference genome">
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365 <option value="cached">locally cached</option>
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366 <option value="history">in your history</option>
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367 </param>
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368 <when value="cached">
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369 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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370 <options from_data_table="lastz_seqs">
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371 <filter type="sort_by" column="1" />
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372 <validator type="no_options" message="No indexes are available." />
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373 </options>
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374 </param>
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375 </when>
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376 <when value="history">
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377 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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378 </when>
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379 </conditional>
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380 </xml>
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381
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382 <token name="@reference_genome_source@">
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383 #if $source.ref_source=="history":
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384 --genome $source.input1
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385 #else:
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386 --genome "$source.input1_2bit.fields.path"
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387 #end if
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388 </token>
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389
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390 <xml name="effectiveGenomeSize">
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391 <conditional name="effectiveGenomeSize">
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392 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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393 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
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394 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
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395 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
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396 <option value="93260000">ce10 (93260000)</option>
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397 <option value="121400000">dm3 (121400000)</option>
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398 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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399 <option value="2150570000">mm9 (2150570000)</option>
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400 <option value="specific">user specified</option>
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401 </param>
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402 <when value="specific">
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403 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
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404 </when>
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405 <when value="2150570000" />
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406 <when value="2451960000" />
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407 <when value="121400000" />
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408 <when value="93260000" />
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409 </conditional>
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410 </xml>
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411
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412 <xml name="skipNAs">
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413 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
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414 label="Ignore missing data?"
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415 help="This parameter determines if non-covered regions
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416 (regions without overlapping reads) in a bam/bigWig file
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417 should be skipped. The default is to treat those
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418 regions as having a value of zero. The decision to
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419 skip non-covered regions depends on the interpretation
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420 of the data. Non-covered regions may represent, for
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421 example, repetitive regions that should be ignored.
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422 (default: False)" />
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423 </xml>
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424
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425 <xml name="input_save_matrix_values">
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426 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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427 </xml>
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428
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429 <xml name="input_graphic_output_settings">
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430 <conditional name="output" >
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431 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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432 <option value="no" selected="true">no</option>
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433 <option value="yes">yes</option>
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434 </param>
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435 <when value="no" />
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436 <when value="yes">
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437 <yield />
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438 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
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439 </when>
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440 </conditional>
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441 </xml>
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442
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443
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444 <xml name="input_image_file_format">
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445 <param argument="--outFileFormat" type="select" label="Image file format">
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446 <option value="png" selected="true">png</option>
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447 <option value="pdf">pdf</option>
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448 <option value="svg">svg</option>
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449 <option value="eps">eps</option>
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450 </param>
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451 </xml>
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452
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453 <xml name="output_image_file_format">
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454 <data format="png" name="outFileName" label="${tool.name} image">
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455 <change_format>
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456 <when input="output.outFileFormat" value="pdf" format="pdf" />
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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457 <when input="output.outFileFormat" value="svg" format="svg" />
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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458 <when input="output.outFileFormat" value="eps" format="eps" />
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459 </change_format>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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460 </data>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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461 </xml>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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462
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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463 <xml name="output_image_file_format_not_nested">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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464 <data format="png" name="outFileName" label="${tool.name} image">
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465 <change_format>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
466 <when input="outFileFormat" value="pdf" format="pdf" />
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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467 <when input="outFileFormat" value="svg" format="svg" />
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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468 <when input="outFileFormat" value="eps" format="eps" />
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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469 </change_format>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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470 </data>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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471 </xml>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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472
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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473 <xml name="output_save_matrix_values">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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474 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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475 <filter>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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476 ((
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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477 output['showOutputSettings'] == 'yes' and
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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478 output['saveMatrix'] is True
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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479 ))
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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480 </filter>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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481 </data>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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482 </xml>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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483
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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484 <xml name="output_graphic_outputs">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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485 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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486 <filter>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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487 ((
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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488 output['showOutputSettings'] == 'yes' and
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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489 output['saveSortedRegions'] is True
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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490 ))
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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491 </filter>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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492 </data>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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493 </xml>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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494
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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495 <xml name="colorMap">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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496 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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497 <option value="RdYlBu" selected="true">RdYlBu</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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498 <option value="Accent">Accent</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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499 <option value="Spectral">Spectral</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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500 <option value="Set1">Set1</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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501 <option value="Set2">Set2</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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502 <option value="Set3">Set3</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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503 <option value="Dark2">Dark2</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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504 <option value="Reds">Reds</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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505 <option value="Oranges">Oranges</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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506 <option value="Greens">Greens</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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507 <option value="Blues">Blues</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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508 <option value="Greys">Greys</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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509 <option value="Purples">Purples</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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510 <option value="Paired">Paired</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
511 <option value="Pastel1">Pastel1</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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512 <option value="Pastel2">Pastel2</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
513 <option value="spring">spring</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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514 <option value="summer">summer</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
515 <option value="autumn">autumn</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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516 <option value="winter">winter</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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517 <option value="hot">hot</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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518 <option value="coolwarm">coolwarm</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
519 <option value="cool">cool</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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520 <option value="seismic">seismic</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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521 <option value="terrain">terrain</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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522 <option value="ocean">ocean</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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523 <option value="rainbow">rainbow</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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524 <option value="bone">bone</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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525 <option value="flag">flag</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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526 <option value="prism">prism</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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527 <option value="cubehelix">cubehelix</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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528 <option value="binary">binary</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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529 <option value="pink">pink</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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530 <option value="gray">gray</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
531 <option value="copper">copper</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
532 <option value="BrBG">BrBG</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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533 <option value="BuGn">BuGn</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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534 <option value="BuPu">BuPu</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
535 <option value="GnBu">GnBu</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
536 <option value="OrRd">OrRd</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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537 <option value="PiYG">PiYG</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
538 <option value="PRGn">PRGn</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
539 <option value="PuOr">PuOr</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
540 <option value="PuRd">PuRd</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
541 <option value="PuBu">PuBu</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
542 <option value="RdBu">RdBu</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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543 <option value="RdGy">RdGy</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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544 <option value="RdPu">RdPu</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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545 <option value="YlGn">YlGn</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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diff changeset
546 <option value="PuBuGn">PuBuGn</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
547 <option value="RdYlGn">RdYlGn</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
548 <option value="YlGnBu">YlGnBu</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
549 <option value="YlOrBr">YlOrBr</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
550 <option value="YlOrRd">YlOrRd</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
551 <option value="gist_gray">gist_gray</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
552 <option value="gist_stern">gist_stern</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
553 <option value="gist_earth">gist_earth</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
554 <option value="gist_yarg">gist_yarg</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
555 <option value="gist_ncar">gist_ncar</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
556 <option value="gist_rainbow">gist_rainbow</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
557 <option value="gist_heat">gist_heat</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
558 <option value="gnuplot">gnuplot</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
559 <option value="gnuplot2">gnuplot2</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
560 <option value="CMRmap">CMRmap</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
561 <option value="bwr">bwr</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
562 <option value="hsv">hsv</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
563 <option value="brg">brg</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
564 <option value="jet">jet</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
565 <option value="afmhot">afmhot</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
566 <option value="Accent_r">Accent reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
567 <option value="Spectral_r">Spectral reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
568 <option value="Set1_r">Set1 reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
569 <option value="Set2_r">Set2 reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
570 <option value="Set3_r">Set3 reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
571 <option value="Dark2_r">Dark2 reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
572 <option value="Reds_r">Reds reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
573 <option value="Oranges_r">Oranges reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
574 <option value="Greens_r">Greens reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
575 <option value="Blues_r">Blues reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
576 <option value="Greys_r">Greys reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
577 <option value="Purples_r">Purples reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
578 <option value="Paired_r">Paired reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
579 <option value="Pastel1_r">Pastel1 reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
580 <option value="Pastel2_r">Pastel2 reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
581 <option value="spring_r">spring reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
582 <option value="summer_r">summer reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
583 <option value="autumn_r">autumn reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
584 <option value="winter_r">winter reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
585 <option value="hot_r">hot reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
586 <option value="coolwarm_r">coolwarm reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
587 <option value="cool_r">cool reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
588 <option value="seismic_r">seismic reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
589 <option value="terrain_r">terrain reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
590 <option value="ocean_r">ocean reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
591 <option value="rainbow_r">rainbow reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
592 <option value="bone_r">bone reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
593 <option value="flag_r">flag reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
594 <option value="prism_r">prism reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
595 <option value="cubehelix_r">cubehelix reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
596 <option value="binary_r">binary reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
597 <option value="pink_r">pink reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
598 <option value="gray_r">gray reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
599 <option value="copper_r">copper reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
600 <option value="BrBG_r">BrBG reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
601 <option value="BuGn_r">BuGn reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
602 <option value="BuPu_r">BuPu reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
603 <option value="GnBu_r">GnBu reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
604 <option value="OrRd_r">OrRd reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
605 <option value="PiYG_r">PiYG reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
606 <option value="PRGn_r">PRGn reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
607 <option value="PuOr_r">PuOr reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
608 <option value="PuRd_r">PuRd reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
609 <option value="PuBu_r">PuBu reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
610 <option value="RdBu_r">RdBu reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
611 <option value="RdGy_r">RdGy reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
612 <option value="RdPu_r">RdPu reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
613 <option value="YlGn_r">YlGn reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
614 <option value="PuBuGn_r">PuBuGn reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
615 <option value="RdYlBu_r">RdYlBu reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
616 <option value="RdYlGn_r">RdYlGn reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
617 <option value="YlGnBu_r">YlGnBu reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
618 <option value="YlOrBr_r">YlOrBr reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
619 <option value="YlOrRd_r">YlOrRd reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
620 <option value="gist_gray_r">gist_gray reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
621 <option value="gist_stern_r">gist_stern reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
622 <option value="gist_earth_r">gist_earth reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
623 <option value="gist_yarg_r">gist_yarg reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
624 <option value="gist_ncar_r">gist_ncar reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
625 <option value="gist_rainbow_r">gist_rainbow reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
626 <option value="gist_heat_r">gist_heat reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
627 <option value="gnuplot_r">gnuplot reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
628 <option value="gnuplot2_r">gnuplot2 reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
629 <option value="CMRmap_r">CMRmap reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
630 <option value="bwr_r">bwr reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
631 <option value="hsv_r">hsv reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents:
diff changeset
632 <option value="brg_r">brg reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
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633 <option value="jet_r">jet reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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634 <option value="afmhot_r">afmhot reversed</option>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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635 </param>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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636
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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637 </xml>
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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638
263b4adf3520 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
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639 </macros>