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annotate deepTools_macros.xml @ 11:485f55e21539 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit beb75870e99ed8ceca69753bf7de546877b3e2ff
author bgruening
date Fri, 12 Aug 2016 05:12:06 -0400
parents 024e6f9762af
children bb00146fa60a
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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 #if $advancedOpt.minFragmentLength:
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34 --minFragmentLength $advancedOpt.minFragmentLength
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35 #end if
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36 #if $advancedOpt.maxFragmentLength:
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37 --maxFragmentLength $advancedOpt.maxFragmentLength
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38 #end if
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39 </token>
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40
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41 <token name="@ADVANCED_OPTS_GTF@">
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42 $advancedOpt.metagene
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43 #if $advancedOpt.transcriptID:
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44 --transcriptID $advancedOpt.transcriptID
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45 #end if
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46 #if $advancedOpt.exonID:
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47 --exonID $advancedOpt.exonID
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48 #end if
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49 #if $advancedOpt.transcript_id_designator:
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50 --transcript_id_designator $advancedOpt.transcript_id_designator
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51 #end if
0
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52 </token>
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53
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54 <xml name="heatmap_options">
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55 <expand macro="zMin_zMax" />
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56 <expand macro="colorMap" />
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57 <expand macro="plotTitle" />
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58 <expand macro="plotNumbers" />
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59 </xml>
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60
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61 <token name="@HEATMAP_OPTIONS@">
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62 #if str($plotting_type.zMin) != "":
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63 --zMin $plotting_type.zMin
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64 #end if
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65 #if str($plotting_type.zMax) != "":
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66 --zMax $plotting_type.zMax
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67 #end if
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68 --colorMap '$plotting_type.colorMap'
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69 $plotting_type.plotNumbers
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70 --plotTitle '$plotting_type.plotTitle'
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71 </token>
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72
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73
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74 <xml name="includeZeros">
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75 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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76 label="Include zeros"
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77 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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78 </xml>
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79
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80 <xml name="zMin_zMax">
10
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81 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0
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82 help="If not specified the value is set automatically."/>
10
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83 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0
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84 help="If not specified the value is set automatically."/>
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85 </xml>
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86
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87 <xml name="region_limit_operation">
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88 <param argument="--region" type="text" value=""
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89 label="Region of the genome to limit the operation to"
8
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90 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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91 <sanitizer>
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92 <valid initial="string.letters,string.digits">
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93 <add value="|"/>
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94 </valid>
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95 </sanitizer>
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96 </param>
0
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97 </xml>
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98
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99 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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100 <token name="@WRAPPER_VERSION@">2.3.3</token>
0
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101 <xml name="requirements">
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102 <requirements>
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103 <requirement type="package" version="2.7.10">python</requirement>
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104 <requirement type="package" version="2.3.3">deepTools</requirement>
0
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105 <yield />
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106 </requirements>
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107 <expand macro="stdio" />
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108 <version_command>@BINARY@ --version</version_command>
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109 </xml>
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110
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111 <xml name="smoothLength">
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112 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
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113 label="Smooth values using the following length (in bases)"
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114 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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115 </xml>
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116
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117
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118 <xml name="kmeans_clustering">
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119 <conditional name="used_multiple_regions">
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120 <param name="used_multiple_regions_options" type="select"
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121 label="Did you compute the matrix with more than one groups of regions?"
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122 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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123 <option value="yes">Yes, I used multiple groups of regions</option>
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124 <option value="no">No, I used only one group</option>
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125 </param>
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126 <when value="no">
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127 <conditional name="clustering">
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128 <param name="clustering_options" type="select" label="Clustering algorithm">
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129 <option value="none">No clustering</option>
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130 <option value="kmeans">Kmeans clustering</option>
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131 <option value="hclust">Hierarchical clustering</option>
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132 </param>
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133 <when value="kmeans">
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134 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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135 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
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136 This only works for data that is not grouped, otherwise only the first group will be clustered.
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137 If more specific clustering methods are required it is advisable to save the underlying matrix and
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138 run the clustering using other software."/>
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139 </when>
2
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140 <when value="hclust">
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141 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
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142 help="WARNING: This option causes the tool to run for a very long time! When this option is
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143 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
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144 This only works for data that is not grouped, otherwise only the first group will be clustered.
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145 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
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146 If more specific clustering methods are required it is advisable to save the underlying matrix and
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147 run the clustering using other software."/>
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148 </when>
0
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149 <when value="none" />
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150 </conditional>
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151 </when>
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152 <when value="yes" />
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153 </conditional>
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154 </xml>
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155
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156 <token name="@KMEANS_CLUSTERING@">
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157 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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158 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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159 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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160 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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161 #end if
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162 #end if
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163 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
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164 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
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165 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
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166 #end if
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167 #end if
0
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168 #end if
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169 </token>
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170
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171 <xml name="samFlags">
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172 <param argument="--samFlagInclude" type="integer" optional="True" value=""
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173 label="Include reads based on the SAM flag"
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174 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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175 <param argument="--samFlagExclude" type="integer" optional="True" value=""
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176 label="Exclude reads based on the SAM flag"
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177 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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178 </xml>
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179
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180 <xml name="fragLength">
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181 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
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182 label="Minimum fragment length for inclusion."
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183 help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
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184 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
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185 label="Maximum fragment length for inclusion."
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186 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
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187 </xml>
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188
0
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189 <xml name="read_processing_options">
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190 <expand macro="extendReads" />
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191 <expand macro="ignoreDuplicates" />
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192 <expand macro="centerReads" />
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193 <expand macro="minMappingQuality" />
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194 <expand macro="samFlags" />
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195 <expand macro="fragLength" />
0
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196 </xml>
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197
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198 <xml name="gtf_options">
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199 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
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200 label="Use a metagene model"
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201 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
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202 <param argument="--transcriptID" optional="True" value="transcript" type="text"
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203 label="trascript designator"
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204 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
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205 <param argument="--exonID" optional="True" value="exon" type="text"
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206 label="exon designator"
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207 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
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208 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
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209 label="transcriptID key designator"
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210 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
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211 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
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212 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
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213 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
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214 </xml>
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215
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216
0
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217 <xml name="plotNumbers">
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218 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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219 label="Plot the correlation value"
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220 help="If set, then the correlation number is plotted on top of the heatmap."/>
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221 </xml>
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222
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223 <xml name="extendReads">
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224 <conditional name="doExtendCustom">
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225 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
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226 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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227 By default *each* read mate is extended.
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228 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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229 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
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230 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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231 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
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232 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
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233 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
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234 <option value="custom">A custom length, which will be applied to ALL reads.</option>
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235 </param>
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236 <when value="no" />
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237 <when value="yes" />
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238 <when value="custom">
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239 <param name="extendReadsValue" type="integer" value="300" min="1"
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240 label="Extend reads to the given average fragment size"
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241 help="Extend all reads to this length" />
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242 </when>
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243 </conditional>
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244 </xml>
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245
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246 <xml name="corMethod">
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247 <param argument="--corMethod" type="select" label="Correlation method">
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248 <option value="spearman" selected="True">Spearman</option>
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249 <option value="pearson">Pearson</option>
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250 </param>
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251 </xml>
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252
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253 <xml name="distanceBetweenBins">
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254 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
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255 label="Distance between bins"
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256 help="By default, multiBamSummary considers consecutive bins of
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257 the specified 'Bin size'. However, to reduce the
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258 computation time, a larger distance between bins can
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259 be given. Larger distances result in fewer bins being
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260 considered."/>
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261 </xml>
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262
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263 <xml name="centerReads">
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264 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
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265 label="Center regions with respect to the fragment length"
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266 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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267 </xml>
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268
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269 <xml name="ignoreDuplicates">
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270 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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271 label="Ignore duplicates"
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272 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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273 </xml>
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274
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275 <xml name="sortUsing">
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276 <param argument="--sortUsing" type="select" label="Method used for sorting"
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277 help="For each row the method is computed.">
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278 <option value="mean" selected="true">mean</option>
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279 <option value="median">median</option>
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280 <option value="min">min</option>
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281 <option value="max">max</option>
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282 <option value="sum">sum</option>
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283 <option value="region_length">region length</option>
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284 </param>
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285 </xml>
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286
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287 <xml name="sortRegions">
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288 <param argument="--sortRegions" type="select" label="Sort regions"
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289 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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290 <option value="no">no ordering</option>
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291 <option value="descend" selected="true">descending order</option>
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292 <option value="ascend">ascending order</option>
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293 </param>
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294 </xml>
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295
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296 <xml name="minMappingQuality">
10
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297 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0
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298 label="Minimum mapping quality"
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299 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
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300 </xml>
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301
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302 <xml name="skipZeros">
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303 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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304 label ="Skip zeros"
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305 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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306 </xml>
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307
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308 <xml name="fragmentLength">
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309 <param argument="--fragmentLength" type="integer" value="300" min="1"
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310 label="Fragment length used for the sequencing"
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311 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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312 </xml>
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313
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314 <xml name="scaleFactor">
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315 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
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316 help="When used in combination with --normalizeTo1x or
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317 --normalizeUsingRPKM, the computed scaling factor will
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318 be multiplied by the given scale factor." />
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319 </xml>
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320
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321 <xml name="scaleFactors">
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322 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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323 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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324 </xml>
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325
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326 <xml name="stdio">
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327 <stdio>
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328 <exit_code range="1:" />
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329 <exit_code range=":-1" />
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330 <regex match="Error:" />
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331 <regex match="Exception:" />
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332 <regex match="EXception:" />
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333 <regex match="Traceback" />
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334 </stdio>
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335 </xml>
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336
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337 <xml name="pseudocount">
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338 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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339 </xml>
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340
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341 <token name="@REFERENCES@">
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342
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343 .. class:: infomark
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344
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345 For more information on the tools, please visit our `help site`_.
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346
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347 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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348
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349 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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350
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351 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
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352 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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353 .. _help site: https://deeptools.readthedocs.org/
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354
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355 </token>
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356 <xml name="citations">
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357 <citations>
8
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358 <citation type="doi">10.1093/nar/gkw257</citation>
0
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359 <yield />
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360 </citations>
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361 </xml>
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362
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363 <xml name="multiple_input_bams">
3
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364 <param argument="--bamfiles" type="data" format="bam" min="1"
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365 label="Bam file" multiple="true"
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366 help=""/>
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367 </xml>
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368
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369 <xml name="multiple_input_bams_min2">
0
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370 <param argument="--bamfiles" type="data" format="bam" min="2"
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371 label="Bam file" multiple="true"
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372 help=""/>
0
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373 </xml>
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374
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375 <xml name="multiple_input_bigwigs">
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376 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
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377 label="Bigwig file"
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378 help="A Bigwig file."/>
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379 </xml>
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380
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381 <xml name="plotTitle">
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382 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
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383 label="Title of the plot"
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384 help="Title of the plot, to be printed on top of the generated image." />
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385 </xml>
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386
2
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387
0
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388 <token name="@multiple_input_bams@">
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389 <![CDATA[
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390 #set files=[]
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391 #set labels=[]
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392 #for $counter, $bamfile in enumerate($bamfiles):
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393 ln -s "${bamfile}" "./${counter}.bam" &&
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394 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
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395 #silent $files.append('%s.bam' % $counter)
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396 #silent $labels.append("'%s'" % ($bamfile.display_name))
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397 #end for
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398 ]]>
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399 </token>
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400
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401 <token name="@multiple_input_bigwigs@">
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402 <![CDATA[
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403 #set files=[]
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404 #set labels=[]
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405 #for $counter, $bigwig in enumerate($bigwigfiles):
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406 ln -s "${bigwig}" "${counter}.bw" &&
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407 #silent $files.append('%s.bw' % $counter)
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408 #silent $labels.append("'%s'" % ($bigwig.display_name))
0
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409 #end for
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410 ]]>
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411 </token>
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412
10
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413 <xml name="blacklist">
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414 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
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415 label="Blacklisted regions in BED/GTF format"
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416 help="One or more files containing regions to exclude from the analysis" />
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417 </xml>
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418
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419 <token name="@blacklist@">
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420 <![CDATA[
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421 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
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422 #set blfiles=[]
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423 #for $f in $advancedOpt.blackListFileName:
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424 #silent $blfiles.append("'%s'" % $f)
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425 #end for
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426 #if $blfiles != ["'None'"]:
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427 --blackListFileName #echo ' '.join($blfiles)#
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428 #end if
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429 #end if
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430 ]]>
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431 </token>
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432
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433 <xml name="multiple_bed">
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434 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
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435 label="Regions in BED/GTF format"
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436 help="One or more files containing regions to include in the analysis" />
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437 </xml>
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438
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439 <token name="@multiple_bed@">
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440 <![CDATA[
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441 #set files=[]
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442 #set labels=[]
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443 #for $f in $BED:
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444 #silent $files.append("'%s'" % $f)
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445 #silent $labels.append("'%s'" % $f.display_name)
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446 #end for
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447 #if len($files) > 0:
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448 --BED #echo ' '.join($files)#
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449 --regionLabels #echo ' '.join($labels)#
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450 #end if
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451 ]]>
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452 </token>
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453
0
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454 <xml name="reference_genome_source">
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455 <conditional name="source">
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456 <param name="ref_source" type="select" label="Reference genome">
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457 <option value="cached">locally cached</option>
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458 <option value="history">in your history</option>
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459 </param>
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460 <when value="cached">
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461 <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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462 <options from_data_table="lastz_seqs">
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463 <filter type="sort_by" column="1" />
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464 <validator type="no_options" message="No indexes are available." />
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465 </options>
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466 </param>
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467 </when>
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468 <when value="history">
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469 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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470 </when>
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471 </conditional>
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472 </xml>
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473
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474 <token name="@reference_genome_source@">
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475 #if $source.ref_source=="history":
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476 --genome $source.input1
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477 #else:
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478 --genome "$source.input1_2bit.fields.path"
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479 #end if
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480 </token>
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481
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482 <xml name="effectiveGenomeSize">
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483 <conditional name="effectiveGenomeSize">
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484 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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485 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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486 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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487 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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488 <option value="93260000">ce10 (93260000)</option>
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489 <option value="121400000">dm3 (121400000)</option>
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490 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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491 <option value="2150570000">mm9 (2150570000)</option>
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492 <option value="specific">user specified</option>
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493 </param>
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494 <when value="specific">
10
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495 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
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496 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
0
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497 </when>
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498 <when value="2150570000" />
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499 <when value="2451960000" />
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500 <when value="121400000" />
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501 <when value="93260000" />
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502 </conditional>
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503 </xml>
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504
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505 <xml name="skipNAs">
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506 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
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507 label="Ignore missing data?"
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508 help="This parameter determines if non-covered regions
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509 (regions without overlapping reads) in a bam/bigWig file
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510 should be skipped. The default is to treat those
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511 regions as having a value of zero. The decision to
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512 skip non-covered regions depends on the interpretation
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513 of the data. Non-covered regions may represent, for
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514 example, repetitive regions that should be ignored.
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515 (default: False)" />
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516 </xml>
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517
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518 <xml name="input_save_matrix_values">
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519 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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520 </xml>
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521
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522 <xml name="input_graphic_output_settings">
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523 <conditional name="output" >
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524 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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525 <option value="no" selected="true">no</option>
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526 <option value="yes">yes</option>
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527 </param>
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528 <when value="no" />
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529 <when value="yes">
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530 <yield />
10
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531 <param name="saveSortedRegions" type="boolean"
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532 label="Save the regions after skipping zeros or min/max threshold values"
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533 help="The order of the regions in the file follows the sorting order selected. This is useful,
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534 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0
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535 </when>
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536 </conditional>
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537 </xml>
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538
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539
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540 <xml name="input_image_file_format">
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541 <param argument="--outFileFormat" type="select" label="Image file format">
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542 <option value="png" selected="true">png</option>
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543 <option value="pdf">pdf</option>
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544 <option value="svg">svg</option>
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545 <option value="eps">eps</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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546 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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diff changeset
547 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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548
10
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
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diff changeset
549 <xml name="output_dpi">
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
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diff changeset
550 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
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diff changeset
551 label="Image dpi" help=""/>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
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diff changeset
552 </xml>
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
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diff changeset
553
0
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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554 <xml name="output_image_file_format">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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555 <data format="png" name="outFileName" label="${tool.name} image">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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556 <change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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557 <when input="output.outFileFormat" value="pdf" format="pdf" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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558 <when input="output.outFileFormat" value="svg" format="svg" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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559 <when input="output.outFileFormat" value="eps" format="eps" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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diff changeset
560 </change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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561 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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562 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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563
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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564 <xml name="output_image_file_format_not_nested">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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diff changeset
565 <data format="png" name="outFileName" label="${tool.name} image">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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566 <change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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567 <when input="outFileFormat" value="pdf" format="pdf" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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568 <when input="outFileFormat" value="svg" format="svg" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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569 <when input="outFileFormat" value="eps" format="eps" />
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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570 </change_format>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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571 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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572 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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573
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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574 <xml name="output_save_matrix_values">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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575 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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576 <filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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577 ((
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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578 output['showOutputSettings'] == 'yes' and
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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579 output['saveMatrix'] is True
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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580 ))
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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581 </filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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582 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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583 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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584
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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585 <xml name="output_graphic_outputs">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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586 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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587 <filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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588 ((
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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589 output['showOutputSettings'] == 'yes' and
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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590 output['saveSortedRegions'] is True
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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591 ))
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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592 </filter>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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593 </data>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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594 </xml>
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595
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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596 <xml name="colorMap">
10
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diff changeset
597 <param name="colorMap" type="select" label="Color map to use for the heatmap"
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diff changeset
598 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
024e6f9762af planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
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599 multiple="true">
0
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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600 <option value="RdYlBu" selected="true">RdYlBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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601 <option value="Accent">Accent</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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602 <option value="Spectral">Spectral</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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603 <option value="Set1">Set1</option>
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604 <option value="Set2">Set2</option>
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605 <option value="Set3">Set3</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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606 <option value="Dark2">Dark2</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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607 <option value="Reds">Reds</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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608 <option value="Oranges">Oranges</option>
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609 <option value="Greens">Greens</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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610 <option value="Blues">Blues</option>
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611 <option value="Greys">Greys</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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612 <option value="Purples">Purples</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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613 <option value="Paired">Paired</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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614 <option value="Pastel1">Pastel1</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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615 <option value="Pastel2">Pastel2</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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616 <option value="spring">spring</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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617 <option value="summer">summer</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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618 <option value="autumn">autumn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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619 <option value="winter">winter</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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620 <option value="hot">hot</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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621 <option value="coolwarm">coolwarm</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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622 <option value="cool">cool</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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623 <option value="seismic">seismic</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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624 <option value="terrain">terrain</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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625 <option value="ocean">ocean</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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626 <option value="rainbow">rainbow</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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627 <option value="bone">bone</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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628 <option value="flag">flag</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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629 <option value="prism">prism</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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630 <option value="cubehelix">cubehelix</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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631 <option value="binary">binary</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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632 <option value="pink">pink</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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633 <option value="gray">gray</option>
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634 <option value="copper">copper</option>
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635 <option value="BrBG">BrBG</option>
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parents:
diff changeset
636 <option value="BuGn">BuGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
637 <option value="BuPu">BuPu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
638 <option value="GnBu">GnBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
639 <option value="OrRd">OrRd</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
640 <option value="PiYG">PiYG</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
641 <option value="PRGn">PRGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
642 <option value="PuOr">PuOr</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
643 <option value="PuRd">PuRd</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
644 <option value="PuBu">PuBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
645 <option value="RdBu">RdBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
646 <option value="RdGy">RdGy</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
647 <option value="RdPu">RdPu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
648 <option value="YlGn">YlGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
649 <option value="PuBuGn">PuBuGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
650 <option value="RdYlGn">RdYlGn</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
651 <option value="YlGnBu">YlGnBu</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
652 <option value="YlOrBr">YlOrBr</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
653 <option value="YlOrRd">YlOrRd</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
654 <option value="gist_gray">gist_gray</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
655 <option value="gist_stern">gist_stern</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
656 <option value="gist_earth">gist_earth</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
657 <option value="gist_yarg">gist_yarg</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
658 <option value="gist_ncar">gist_ncar</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
659 <option value="gist_rainbow">gist_rainbow</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
660 <option value="gist_heat">gist_heat</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
661 <option value="gnuplot">gnuplot</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
662 <option value="gnuplot2">gnuplot2</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
663 <option value="CMRmap">CMRmap</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
664 <option value="bwr">bwr</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
665 <option value="hsv">hsv</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
666 <option value="brg">brg</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
667 <option value="jet">jet</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
668 <option value="afmhot">afmhot</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
669 <option value="Accent_r">Accent reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
670 <option value="Spectral_r">Spectral reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
671 <option value="Set1_r">Set1 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
672 <option value="Set2_r">Set2 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
673 <option value="Set3_r">Set3 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
674 <option value="Dark2_r">Dark2 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
675 <option value="Reds_r">Reds reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
676 <option value="Oranges_r">Oranges reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
677 <option value="Greens_r">Greens reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
678 <option value="Blues_r">Blues reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
679 <option value="Greys_r">Greys reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
680 <option value="Purples_r">Purples reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
681 <option value="Paired_r">Paired reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
682 <option value="Pastel1_r">Pastel1 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
683 <option value="Pastel2_r">Pastel2 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
684 <option value="spring_r">spring reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
685 <option value="summer_r">summer reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
686 <option value="autumn_r">autumn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
687 <option value="winter_r">winter reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
688 <option value="hot_r">hot reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
689 <option value="coolwarm_r">coolwarm reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
690 <option value="cool_r">cool reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
691 <option value="seismic_r">seismic reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
692 <option value="terrain_r">terrain reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
693 <option value="ocean_r">ocean reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
694 <option value="rainbow_r">rainbow reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
695 <option value="bone_r">bone reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
696 <option value="flag_r">flag reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
697 <option value="prism_r">prism reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
698 <option value="cubehelix_r">cubehelix reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
699 <option value="binary_r">binary reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
700 <option value="pink_r">pink reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
701 <option value="gray_r">gray reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
702 <option value="copper_r">copper reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
703 <option value="BrBG_r">BrBG reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
704 <option value="BuGn_r">BuGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
705 <option value="BuPu_r">BuPu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
706 <option value="GnBu_r">GnBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
707 <option value="OrRd_r">OrRd reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
708 <option value="PiYG_r">PiYG reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
709 <option value="PRGn_r">PRGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
710 <option value="PuOr_r">PuOr reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
711 <option value="PuRd_r">PuRd reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
712 <option value="PuBu_r">PuBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
713 <option value="RdBu_r">RdBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
714 <option value="RdGy_r">RdGy reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
715 <option value="RdPu_r">RdPu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
716 <option value="YlGn_r">YlGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
717 <option value="PuBuGn_r">PuBuGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
718 <option value="RdYlBu_r">RdYlBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
719 <option value="RdYlGn_r">RdYlGn reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
720 <option value="YlGnBu_r">YlGnBu reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
721 <option value="YlOrBr_r">YlOrBr reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
722 <option value="YlOrRd_r">YlOrRd reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
723 <option value="gist_gray_r">gist_gray reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
724 <option value="gist_stern_r">gist_stern reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
725 <option value="gist_earth_r">gist_earth reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
726 <option value="gist_yarg_r">gist_yarg reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
727 <option value="gist_ncar_r">gist_ncar reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
728 <option value="gist_rainbow_r">gist_rainbow reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
729 <option value="gist_heat_r">gist_heat reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
730 <option value="gnuplot_r">gnuplot reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
731 <option value="gnuplot2_r">gnuplot2 reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
732 <option value="CMRmap_r">CMRmap reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
733 <option value="bwr_r">bwr reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
734 <option value="hsv_r">hsv reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
735 <option value="brg_r">brg reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
736 <option value="jet_r">jet reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
737 <option value="afmhot_r">afmhot reversed</option>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
738 </param>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
739
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
740 </xml>
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
bgruening
parents:
diff changeset
741
812bfd545d3a planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
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parents:
diff changeset
742 </macros>