annotate deepTools_macros.xml @ 17:68932756bf49 draft

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1 <macros>
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2
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3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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4 <token name="@WRAPPER_VERSION@">3.0.0</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="3.0.0">deeptools</requirement>
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8 <requirement type="package" version="1.7">samtools</requirement>
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9 </requirements>
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10 <expand macro="stdio" />
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11 <version_command>@BINARY@ --version</version_command>
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12 </xml>
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13
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14 <xml name="advancedOpt_scaffold">
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15 <conditional name="advancedOpt">
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16 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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17 <option value="no" selected="true">no</option>
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18 <option value="yes">yes</option>
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19 </param>
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20 <when value="no" />
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21 <when value="yes">
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22 <yield/>
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23 </when>
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24 </conditional>
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25 </xml>
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26
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27 <token name="@PLOTWIDTHHEIGHT@">
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28 --plotWidth '$advancedOpt.plotWidth'
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29 --plotHeight '$advancedOpt.plotHeight'
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30 </token>
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31
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32 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
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33 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
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34 label="Plot height"
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35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
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36
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37 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
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38 label="Plot width"
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39 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
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40 </xml>
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41
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42 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
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43 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
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44 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
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45 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
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46 --extendReads
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47 #end if
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48 $advancedOpt.ignoreDuplicates
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49 $advancedOpt.centerReads
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50 #if $advancedOpt.minMappingQuality:
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51 --minMappingQuality '$advancedOpt.minMappingQuality'
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52 #end if
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53 #if $advancedOpt.samFlagInclude:
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54 --samFlagInclude $advancedOpt.samFlagInclude
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55 #end if
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56 #if $advancedOpt.samFlagExclude:
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57 --samFlagExclude $advancedOpt.samFlagExclude
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58 #end if
8
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59 #if $advancedOpt.minFragmentLength:
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60 --minFragmentLength $advancedOpt.minFragmentLength
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61 #end if
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62 #if $advancedOpt.maxFragmentLength:
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63 --maxFragmentLength $advancedOpt.maxFragmentLength
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64 #end if
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65 </token>
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66
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67 <token name="@ADVANCED_OPTS_GTF@">
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68 $advancedOpt.metagene
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69 #if $advancedOpt.transcriptID:
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70 --transcriptID $advancedOpt.transcriptID
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71 #end if
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72 #if $advancedOpt.exonID:
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73 --exonID $advancedOpt.exonID
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74 #end if
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75 #if $advancedOpt.transcript_id_designator:
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76 --transcript_id_designator $advancedOpt.transcript_id_designator
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77 #end if
0
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78 </token>
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79
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80 <xml name="heatmap_options">
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81 <expand macro="zMin_zMax" />
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82 <expand macro="colorMap" />
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83 <expand macro="plotTitle" />
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84 <expand macro="plotNumbers" />
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85 </xml>
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86
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87 <token name="@HEATMAP_OPTIONS@">
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88 #if str($plotting_type.zMin) != "":
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89 --zMin $plotting_type.zMin
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90 #end if
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91 #if str($plotting_type.zMax) != "":
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92 --zMax $plotting_type.zMax
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93 #end if
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94 --colorMap '$plotting_type.colorMap'
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95 $plotting_type.plotNumbers
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96 --plotTitle '$plotting_type.plotTitle'
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97 </token>
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98
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99
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100 <xml name="includeZeros">
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101 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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102 label="Include zeros"
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103 help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />
0
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104 </xml>
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105
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106 <xml name="zMin_zMax">
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107 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0
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108 help="If not specified the value is set automatically."/>
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109 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0
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110 help="If not specified the value is set automatically."/>
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111 </xml>
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112
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113 <xml name="region_limit_operation">
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114 <param argument="--region" type="text" value=""
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115 label="Region of the genome to limit the operation to"
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116 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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117 <sanitizer>
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118 <valid initial="string.letters,string.digits">
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119 <add value="|"/>
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120 <add value=":"/>
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121 </valid>
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122 </sanitizer>
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123 </param>
0
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124 </xml>
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125
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126 <xml name="smoothLength">
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127 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
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128 label="Smooth values using the following length (in bases)"
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129 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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130 </xml>
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131
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132
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133 <xml name="kmeans_clustering">
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134 <conditional name="used_multiple_regions">
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135 <param name="used_multiple_regions_options" type="select"
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136 label="Did you compute the matrix with more than one groups of regions?"
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137 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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138 <option value="yes">Yes, I used multiple groups of regions</option>
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139 <option value="no">No, I used only one group</option>
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140 </param>
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141 <when value="no">
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142 <conditional name="clustering">
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143 <param name="clustering_options" type="select" label="Clustering algorithm">
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144 <option value="none">No clustering</option>
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145 <option value="kmeans">Kmeans clustering</option>
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146 <option value="hclust">Hierarchical clustering</option>
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147 </param>
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148 <when value="kmeans">
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149 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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150 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
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151 This only works for data that is not grouped, otherwise only the first group will be clustered.
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152 If more specific clustering methods are required it is advisable to save the underlying matrix and
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153 run the clustering using other software."/>
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154 </when>
1
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155 <when value="hclust">
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156 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
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157 help="WARNING: This option causes the tool to run for a very long time! When this option is
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158 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
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159 This only works for data that is not grouped, otherwise only the first group will be clustered.
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160 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
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161 If more specific clustering methods are required it is advisable to save the underlying matrix and
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162 run the clustering using other software."/>
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163 </when>
0
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164 <when value="none" />
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165 </conditional>
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166 </when>
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167 <when value="yes" />
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168 </conditional>
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169 </xml>
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170
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171 <token name="@KMEANS_CLUSTERING@">
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172 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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173 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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174 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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175 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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176 #end if
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177 #end if
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178 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
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179 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
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180 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
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181 #end if
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182 #end if
0
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183 #end if
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184 </token>
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185
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186 <xml name="samFlags">
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187 <param argument="--samFlagInclude" type="integer" optional="True" value=""
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188 label="Include reads based on the SAM flag"
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189 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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190 <param argument="--samFlagExclude" type="integer" optional="True" value=""
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191 label="Exclude reads based on the SAM flag"
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192 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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193 </xml>
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194
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195 <xml name="fragLength">
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196 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
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197 label="Minimum fragment length for inclusion."
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198 help="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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199 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
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200 label="Maximum fragment length for inclusion."
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201 help="A value of 0 (the default) is equivalent to no maximum." />
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202 </xml>
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203
0
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204 <xml name="read_processing_options">
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205 <expand macro="extendReads" />
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206 <expand macro="ignoreDuplicates" />
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207 <expand macro="centerReads" />
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208 <expand macro="minMappingQuality" />
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209 <expand macro="samFlags" />
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210 <expand macro="fragLength" />
0
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211 </xml>
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212
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213 <xml name="gtf_options">
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214 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
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215 label="Use a metagene model"
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216 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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217 <param argument="--transcriptID" optional="True" value="transcript" type="text"
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218 label="trascript designator"
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219 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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220 <param argument="--exonID" optional="True" value="exon" type="text"
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221 label="exon designator"
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222 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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223 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
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224 label="transcriptID key designator"
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225 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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226 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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227 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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228 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
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229 </xml>
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230
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231
0
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232 <xml name="plotNumbers">
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233 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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234 label="Plot the correlation value"
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235 help="If set, then the correlation number is plotted on top of the heatmap."/>
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236 </xml>
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237
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238 <xml name="extendReads">
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239 <conditional name="doExtendCustom">
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240 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
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241 help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
0
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242 By default *each* read mate is extended.
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243 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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244 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
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245 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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246 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
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247 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
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248 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
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249 <option value="custom">A custom length, which will be applied to ALL reads.</option>
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250 </param>
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251 <when value="no" />
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252 <when value="yes" />
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253 <when value="custom">
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254 <param name="extendReadsValue" type="integer" value="300" min="1"
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255 label="Extend reads to the given average fragment size"
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256 help="Extend all reads to this length" />
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257 </when>
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258 </conditional>
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259 </xml>
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260
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261 <xml name="corMethod">
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262 <param argument="--corMethod" type="select" label="Correlation method">
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263 <option value="spearman" selected="True">Spearman</option>
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264 <option value="pearson">Pearson</option>
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265 </param>
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266 </xml>
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267
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268 <xml name="distanceBetweenBins">
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269 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
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270 label="Distance between bins"
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271 help="By default, multiBamSummary considers consecutive bins of
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272 the specified 'Bin size'. However, to reduce the
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273 computation time, a larger distance between bins can
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274 be given. Larger distances result in fewer bins being
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275 considered."/>
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276 </xml>
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277
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278 <xml name="centerReads">
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279 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
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280 label="Center regions with respect to the fragment length"
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281 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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282 </xml>
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283
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284 <xml name="ignoreDuplicates">
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285 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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286 label="Ignore duplicates"
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287 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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288 </xml>
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289
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290 <xml name="sortUsing">
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291 <param argument="--sortUsing" type="select" label="Method used for sorting"
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292 help="For each row the method is computed.">
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293 <option value="mean" selected="true">mean</option>
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294 <option value="median">median</option>
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295 <option value="min">min</option>
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296 <option value="max">max</option>
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297 <option value="sum">sum</option>
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298 <option value="region_length">region length</option>
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299 </param>
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300 </xml>
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301
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302 <xml name="sortRegionsComputeMatrix">
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303 <param argument="--sortRegions" type="select" label="Sort regions"
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304 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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305 <option value="no">no ordering</option>
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306 <option value="keep" selected="true">maintain the same ordering as the input files</option>
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307 <option value="descend">descending order</option>
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308 <option value="ascend">ascending order</option>
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309 </param>
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310 </xml>
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311
0
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312 <xml name="sortRegions">
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313 <param argument="--sortRegions" type="select" label="Sort regions"
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314 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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315 <option value="no">maintain the same ordering as the input files</option>
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316 <option value="descend" selected="true">descending order</option>
0
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317 <option value="ascend">ascending order</option>
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318 </param>
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319 </xml>
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320
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321 <xml name="minMappingQuality">
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322 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0
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323 label="Minimum mapping quality"
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324 help= "If set, only reads with a mapping quality score at least this high are considered."/>
0
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325 </xml>
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326
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327 <xml name="skipZeros">
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328 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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329 label ="Skip zeros"
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330 help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />
0
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331 </xml>
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332
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333 <xml name="fragmentLength">
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334 <param argument="--fragmentLength" type="integer" min="1" optional="true"
0
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335 label="Fragment length used for the sequencing"
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336 help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/>
0
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337 </xml>
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338
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339 <xml name="scaleFactor">
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340 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
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341 help="The computed scaling factor will be multiplied by this (default 1)." />
0
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342 </xml>
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343
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344 <xml name="scaleFactors">
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345 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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346 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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347 </xml>
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348
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349 <xml name="stdio">
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350 <stdio>
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351 <exit_code range="1:" />
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352 <exit_code range=":-1" />
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353 <regex match="Error:" />
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354 <regex match="Exception:" />
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355 <regex match="EXception:" />
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356 <regex match="Traceback" />
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357 </stdio>
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358 </xml>
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359
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360 <xml name="pseudocount">
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361 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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362 </xml>
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363
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364 <token name="@REFERENCES@">
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365
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366 .. class:: infomark
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367
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368 For more information on the tools, please visit our `help site`_.
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369
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370 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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371
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372 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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373
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374 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
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375 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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376 .. _help site: https://deeptools.readthedocs.org/
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377
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378 </token>
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379 <xml name="citations">
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380 <citations>
6
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381 <citation type="doi">10.1093/nar/gkw257</citation>
0
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382 <yield />
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383 </citations>
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384 </xml>
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385
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386 <xml name="multiple_input_bams" tokens="MIN">
10
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387 <conditional name="multibam_conditional">
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388 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
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389 <option value="No" selected="true">No</option>
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390 <option value="Yes">Yes</option>
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391 </param>
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392 <when value="No">
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393 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
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394 label="BAM/CRAM file" multiple="true"
10
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395 help=""/>
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396 </when>
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397 <when value="Yes">
17
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398 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
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399 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
10
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400 </repeat>
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401 </when>
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402 </conditional>
1
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403 </xml>
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404
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405 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
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406 <conditional name="multibigwig_conditional">
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407 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
10
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408 is vital to you, select Yes below.">
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409 <option value="No" selected="true">No</option>
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410 <option value="Yes">Yes</option>
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411 </param>
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412 <when value="No">
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413 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
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414 label="@LABEL@"
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415 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
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416 </when>
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417 <when value="Yes">
14
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418 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
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419 <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
10
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420 </repeat>
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421 </when>
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422 </conditional>
0
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423 </xml>
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424
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425 <xml name="plotTitle">
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426 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
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427 label="Title of the plot"
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428 help="Title of the plot, to be printed on top of the generated image." />
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429 </xml>
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430
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431 <xml name="labelRotation">
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432 <param argument="--labelRotation" type="integer" value="0"
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433 label="Rotation of the X-axis labels (in degrees)"
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434 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
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435 </xml>
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436
1
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437
0
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438 <token name="@multiple_input_bams@">
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439 <![CDATA[
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440 #set files=[]
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441 #set labels=[]
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442 #import re
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443 #if $multibam_conditional.orderMatters == "No":
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444 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
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445 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
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446 ln -s "${bamfile}" "./${counter}.bam" &&
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447 #if $bamfile.ext == 'bam':
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448 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
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449 #else:
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450 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
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451 #end if
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452 #silent $files.append("'%s.bam'" % $counter)
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453 #silent $labels.append("'%s'" % identifier)
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454 #end for
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455 #else:
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456 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
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457 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
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458 ln -s "${f.bamfiles}" "./${counter}.bam" &&
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459 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
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460 #if $f.bamfiles.ext == 'bam':
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461 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
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462 #else:
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463 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
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464 #end if
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465 #silent $files.append("'%s.bam'" % $counter)
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466 #silent $labels.append("'%s'" % $identifier)
10
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467 #end for
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468 #end if
0
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469 ]]>
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470 </token>
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471
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472 <token name="@multiple_input_bigwigs@">
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473 <![CDATA[
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474 #set files=[]
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475 #set labels=[]
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476 #import re
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477 #if $multibigwig_conditional.orderMatters == "No":
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478 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
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479 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
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480 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
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481 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
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482 #silent $labels.append("'%s'" % $identifier)
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483 #end for
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484 #else:
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485 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
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486 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
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487 ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
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488 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
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489 #silent $labels.append("'%s'" % $identifier)
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490 #end for
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491 #end if
0
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492 ]]>
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493 </token>
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494
8
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495 <xml name="blacklist">
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496 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
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497 label="Blacklisted regions in BED/GTF format"
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498 help="One or more files containing regions to exclude from the analysis" />
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499 </xml>
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500
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501 <token name="@blacklist@">
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502 <![CDATA[
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503 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
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504 #set blfiles=[]
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505 #for $f in $advancedOpt.blackListFileName:
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506 #silent $blfiles.append("'%s'" % $f)
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507 #end for
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508 #if $blfiles != ["'None'"]:
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509 --blackListFileName #echo ' '.join($blfiles)#
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510 #end if
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511 #end if
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512 ]]>
8
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513 </token>
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514
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515 <xml name="multiple_bed">
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516 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
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517 label="Regions in BED/GTF format"
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518 help="One or more files containing regions to include in the analysis" />
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519 </xml>
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520
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521 <token name="@multiple_bed@">
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522 <![CDATA[
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523 #set files=[]
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524 #set labels=[]
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525 #for $f in $BED:
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526 #silent $files.append("'%s'" % $f)
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527 #silent $labels.append("'%s'" % $f.display_name)
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528 #end for
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529 #if len($files) > 0:
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530 --BED #echo ' '.join($files)#
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531 --regionLabels #echo ' '.join($labels)#
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532 #end if
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533 ]]>
8
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534 </token>
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535
0
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536 <xml name="reference_genome_source">
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537 <conditional name="source">
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538 <param name="ref_source" type="select" label="Reference genome">
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539 <option value="cached">locally cached</option>
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540 <option value="history">in your history</option>
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541 </param>
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542 <when value="cached">
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543 <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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544 <options from_data_table="lastz_seqs">
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545 <filter type="sort_by" column="1" />
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546 <validator type="no_options" message="No indexes are available." />
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547 </options>
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548 </param>
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549 </when>
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550 <when value="history">
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551 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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552 </when>
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553 </conditional>
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554 </xml>
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555
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556 <token name="@reference_genome_source@">
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557 #if $source.ref_source=="history":
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558 --genome $source.input1
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559 #else:
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560 --genome "$source.input1_2bit.fields.path"
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561 #end if
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562 </token>
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563
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564 <xml name="effectiveGenomeSize">
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565 <conditional name="effectiveGenomeSize">
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566 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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567 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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568 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
17
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569 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
0
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570 <option value="93260000">ce10 (93260000)</option>
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571 <option value="130428560">dm3 (130428560)</option>
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572 <option value="125464728">dm6 (125464728)</option>
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573 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
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574 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
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575 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
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576 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
0
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577 <option value="specific">user specified</option>
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578 </param>
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579 <when value="specific">
8
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580 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
17
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581 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
0
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582 </when>
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583 <when value="93260000" />
17
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584 <when value="130428560" />
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585 <when value="125464728" />
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586 <when value="2685511504" />
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587 <when value="2701495761" />
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588 <when value="2304947926" />
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589 <when value="2308125349" />
0
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590 </conditional>
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591 </xml>
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592
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593 <xml name="skipNAs">
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594 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
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595 label="Ignore missing data?"
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596 help="This parameter determines if non-covered regions
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597 (regions without overlapping reads) in a bam/bigWig file
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598 should be skipped. The default is to treat those
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599 regions as having a value of zero. The decision to
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600 skip non-covered regions depends on the interpretation
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601 of the data. Non-covered regions may represent, for
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602 example, repetitive regions that should be ignored.
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603 (default: False)" />
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604 </xml>
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605
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606 <xml name="input_save_matrix_values">
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607 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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608 </xml>
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609
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610 <xml name="input_graphic_output_settings">
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611 <conditional name="output" >
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612 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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613 <option value="no" selected="true">no</option>
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614 <option value="yes">yes</option>
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615 </param>
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616 <when value="no" />
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617 <when value="yes">
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618 <yield />
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619 <param name="saveSortedRegions" type="boolean"
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620 argument="--outFileSortedRegions"
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621 label="Save the regions after skipping zeros or min/max threshold values"
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622 help="The order of the regions in the file follows the sorting order selected. This is useful,
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623 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0
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624 </when>
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625 </conditional>
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626 </xml>
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627
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628
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629 <xml name="input_image_file_format">
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630 <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
0
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631 <option value="png" selected="true">png</option>
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632 <option value="pdf">pdf</option>
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633 <option value="svg">svg</option>
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634 <option value="eps">eps</option>
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635 <option value="plotly">plotly</option>
0
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636 </param>
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637 </xml>
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638
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639 <xml name="output_dpi">
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640 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
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641 label="Image dpi" help=""/>
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642 </xml>
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643
0
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644 <xml name="output_image_file_format">
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645 <data format="png" name="outFileName" label="${tool.name} image">
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646 <change_format>
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647 <when input="output.outFileFormat" value="pdf" format="pdf" />
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648 <when input="output.outFileFormat" value="svg" format="svg" />
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649 <when input="output.outFileFormat" value="eps" format="eps" />
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650 <when input="output.outFileFormat" value="plotly" format="html" />
0
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651 </change_format>
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652 </data>
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653 </xml>
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654
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655 <xml name="output_image_file_format_not_nested">
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656 <data format="png" name="outFileName" label="${tool.name} image">
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657 <change_format>
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658 <when input="outFileFormat" value="pdf" format="pdf" />
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659 <when input="outFileFormat" value="svg" format="svg" />
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660 <when input="outFileFormat" value="eps" format="eps" />
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661 <when input="outFileFormat" value="plotly" format="html" />
0
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662 </change_format>
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663 </data>
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664 </xml>
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665
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666 <xml name="output_save_matrix_values">
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667 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
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668 <filter>
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669 ((
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670 output['showOutputSettings'] == 'yes' and
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671 output['saveMatrix'] is True
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672 ))
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673 </filter>
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674 </data>
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675 </xml>
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676
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677 <xml name="output_graphic_outputs">
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678 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
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679 <filter>
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680 ((
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681 output['showOutputSettings'] == 'yes' and
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682 output['saveSortedRegions'] is True
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683 ))
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684 </filter>
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685 </data>
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686 </xml>
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687
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688 <xml name="colorMap">
8
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689 <param name="colorMap" type="select" label="Color map to use for the heatmap"
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690 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
0
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diff changeset
691 <option value="RdYlBu" selected="true">RdYlBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
692 <option value="Accent">Accent</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
693 <option value="Spectral">Spectral</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
694 <option value="Set1">Set1</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
695 <option value="Set2">Set2</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
696 <option value="Set3">Set3</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
697 <option value="Dark2">Dark2</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
698 <option value="Reds">Reds</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
699 <option value="Oranges">Oranges</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
700 <option value="Greens">Greens</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
701 <option value="Blues">Blues</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
702 <option value="Greys">Greys</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
703 <option value="Purples">Purples</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
704 <option value="Paired">Paired</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
705 <option value="Pastel1">Pastel1</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
706 <option value="Pastel2">Pastel2</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
707 <option value="spring">spring</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
708 <option value="summer">summer</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
709 <option value="autumn">autumn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
710 <option value="winter">winter</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
711 <option value="hot">hot</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
712 <option value="coolwarm">coolwarm</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
713 <option value="cool">cool</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
714 <option value="seismic">seismic</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
715 <option value="terrain">terrain</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
716 <option value="ocean">ocean</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
717 <option value="rainbow">rainbow</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
718 <option value="bone">bone</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
719 <option value="flag">flag</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
720 <option value="prism">prism</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
721 <option value="cubehelix">cubehelix</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
722 <option value="binary">binary</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
723 <option value="pink">pink</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
724 <option value="gray">gray</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
725 <option value="copper">copper</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
726 <option value="BrBG">BrBG</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
727 <option value="BuGn">BuGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
728 <option value="BuPu">BuPu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
729 <option value="GnBu">GnBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
730 <option value="OrRd">OrRd</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
731 <option value="PiYG">PiYG</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
732 <option value="PRGn">PRGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
733 <option value="PuOr">PuOr</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
734 <option value="PuRd">PuRd</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
735 <option value="PuBu">PuBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
736 <option value="RdBu">RdBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
737 <option value="RdGy">RdGy</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
738 <option value="RdPu">RdPu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
739 <option value="YlGn">YlGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
740 <option value="PuBuGn">PuBuGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
741 <option value="RdYlGn">RdYlGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
742 <option value="YlGnBu">YlGnBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
743 <option value="YlOrBr">YlOrBr</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
744 <option value="YlOrRd">YlOrRd</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
745 <option value="gist_gray">gist_gray</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
746 <option value="gist_stern">gist_stern</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
747 <option value="gist_earth">gist_earth</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
748 <option value="gist_yarg">gist_yarg</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
749 <option value="gist_ncar">gist_ncar</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
750 <option value="gist_rainbow">gist_rainbow</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
751 <option value="gist_heat">gist_heat</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
752 <option value="gnuplot">gnuplot</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
753 <option value="gnuplot2">gnuplot2</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
754 <option value="CMRmap">CMRmap</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
755 <option value="bwr">bwr</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
756 <option value="hsv">hsv</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
757 <option value="brg">brg</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
758 <option value="jet">jet</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
759 <option value="afmhot">afmhot</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
760 <option value="Accent_r">Accent reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
761 <option value="Spectral_r">Spectral reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
762 <option value="Set1_r">Set1 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
763 <option value="Set2_r">Set2 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
764 <option value="Set3_r">Set3 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
765 <option value="Dark2_r">Dark2 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
766 <option value="Reds_r">Reds reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
767 <option value="Oranges_r">Oranges reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
768 <option value="Greens_r">Greens reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
769 <option value="Blues_r">Blues reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
770 <option value="Greys_r">Greys reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
771 <option value="Purples_r">Purples reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
772 <option value="Paired_r">Paired reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
773 <option value="Pastel1_r">Pastel1 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
774 <option value="Pastel2_r">Pastel2 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
775 <option value="spring_r">spring reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
776 <option value="summer_r">summer reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
777 <option value="autumn_r">autumn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
778 <option value="winter_r">winter reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
779 <option value="hot_r">hot reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
780 <option value="coolwarm_r">coolwarm reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
781 <option value="cool_r">cool reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
782 <option value="seismic_r">seismic reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
783 <option value="terrain_r">terrain reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
784 <option value="ocean_r">ocean reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
785 <option value="rainbow_r">rainbow reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
786 <option value="bone_r">bone reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
787 <option value="flag_r">flag reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
788 <option value="prism_r">prism reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
789 <option value="cubehelix_r">cubehelix reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
790 <option value="binary_r">binary reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
791 <option value="pink_r">pink reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
792 <option value="gray_r">gray reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
793 <option value="copper_r">copper reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
794 <option value="BrBG_r">BrBG reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
795 <option value="BuGn_r">BuGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
796 <option value="BuPu_r">BuPu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
797 <option value="GnBu_r">GnBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
798 <option value="OrRd_r">OrRd reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
799 <option value="PiYG_r">PiYG reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
800 <option value="PRGn_r">PRGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
801 <option value="PuOr_r">PuOr reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
802 <option value="PuRd_r">PuRd reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
803 <option value="PuBu_r">PuBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
804 <option value="RdBu_r">RdBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
805 <option value="RdGy_r">RdGy reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
806 <option value="RdPu_r">RdPu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
807 <option value="YlGn_r">YlGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
808 <option value="PuBuGn_r">PuBuGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
809 <option value="RdYlBu_r">RdYlBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
810 <option value="RdYlGn_r">RdYlGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
811 <option value="YlGnBu_r">YlGnBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
812 <option value="YlOrBr_r">YlOrBr reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
813 <option value="YlOrRd_r">YlOrRd reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
814 <option value="gist_gray_r">gist_gray reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
815 <option value="gist_stern_r">gist_stern reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
816 <option value="gist_earth_r">gist_earth reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
817 <option value="gist_yarg_r">gist_yarg reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
818 <option value="gist_ncar_r">gist_ncar reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
819 <option value="gist_rainbow_r">gist_rainbow reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
820 <option value="gist_heat_r">gist_heat reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
821 <option value="gnuplot_r">gnuplot reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
822 <option value="gnuplot2_r">gnuplot2 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
823 <option value="CMRmap_r">CMRmap reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
824 <option value="bwr_r">bwr reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
825 <option value="hsv_r">hsv reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
826 <option value="brg_r">brg reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
827 <option value="jet_r">jet reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
828 <option value="afmhot_r">afmhot reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
829 </param>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
830
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
831 </xml>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
832
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
833 </macros>