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annotate deepTools_macros.xml @ 0:1638c02b28b5 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 08:09:05 -0500
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children 0240a81c3ae6
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1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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1 <macros>
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2
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3 <xml name="advancedOpt_scaffold">
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4 <conditional name="advancedOpt">
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5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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6 <option value="no" selected="true">no</option>
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7 <option value="yes">yes</option>
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8 </param>
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9 <when value="no" />
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10 <when value="yes">
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11 <yield/>
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12 </when>
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13 </conditional>
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14 </xml>
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15
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16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
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17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
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18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
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19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
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20 --extendReads
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21 #end if
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22 $advancedOpt.ignoreDuplicates
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23 $advancedOpt.centerReads
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24 #if $advancedOpt.minMappingQuality:
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25 --minMappingQuality '$advancedOpt.minMappingQuality'
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26 #end if
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27 #if $advancedOpt.samFlagInclude:
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28 --samFlagInclude $advancedOpt.samFlagInclude
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29 #end if
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30 #if $advancedOpt.samFlagExclude:
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31 --samFlagExclude $advancedOpt.samFlagExclude
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32 #end if
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33 #if $advancedOpt.minFragmentLength:
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34 --minFragmentLength $advancedOpt.minFragmentLength
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35 #end if
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36 #if $advancedOpt.maxFragmentLength:
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37 --maxFragmentLength $advancedOpt.maxFragmentLength
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38 #end if
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39 </token>
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40
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41 <token name="@ADVANCED_OPTS_GTF@">
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42 $advancedOpt.metagene
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43 #if $advancedOpt.transcriptID:
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44 --transcriptID $advancedOpt.transcriptID
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45 #end if
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46 #if $advancedOpt.exonID:
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47 --exonID $advancedOpt.exonID
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48 #end if
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49 #if $advancedOpt.transcript_id_designator:
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50 --transcript_id_designator $advancedOpt.transcript_id_designator
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51 #end if
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52 </token>
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53
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54 <xml name="heatmap_options">
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55 <expand macro="zMin_zMax" />
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56 <expand macro="colorMap" />
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57 <expand macro="plotTitle" />
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58 <expand macro="plotNumbers" />
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59 </xml>
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60
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61 <token name="@HEATMAP_OPTIONS@">
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62 #if str($plotting_type.zMin) != "":
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63 --zMin $plotting_type.zMin
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64 #end if
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65 #if str($plotting_type.zMax) != "":
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66 --zMax $plotting_type.zMax
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67 #end if
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68 --colorMap '$plotting_type.colorMap'
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69 $plotting_type.plotNumbers
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70 --plotTitle '$plotting_type.plotTitle'
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71 </token>
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72
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73
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74 <xml name="includeZeros">
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75 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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76 label="Include zeros"
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77 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
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78 </xml>
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79
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80 <xml name="zMin_zMax">
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81 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
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82 help="If not specified the value is set automatically."/>
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83 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
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84 help="If not specified the value is set automatically."/>
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85 </xml>
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86
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87 <xml name="region_limit_operation">
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88 <param argument="--region" type="text" value=""
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89 label="Region of the genome to limit the operation to"
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90 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
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91 <sanitizer>
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92 <valid initial="string.letters,string.digits">
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93 <add value="|"/>
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94 <add value=":"/>
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95 </valid>
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96 </sanitizer>
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97 </param>
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98 </xml>
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99
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100 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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101 <token name="@WRAPPER_VERSION@">2.4.1</token>
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102 <xml name="requirements">
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103 <requirements>
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104 <requirement type="package" version="2.7.10">python</requirement>
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105 <requirement type="package" version="2.4.1">deeptools</requirement>
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106 <yield />
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107 </requirements>
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108 <expand macro="stdio" />
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109 <version_command>@BINARY@ --version</version_command>
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110 </xml>
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111
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112 <xml name="smoothLength">
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113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
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114 label="Smooth values using the following length (in bases)"
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115 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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116 </xml>
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117
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118
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119 <xml name="kmeans_clustering">
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120 <conditional name="used_multiple_regions">
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121 <param name="used_multiple_regions_options" type="select"
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122 label="Did you compute the matrix with more than one groups of regions?"
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123 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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124 <option value="yes">Yes, I used multiple groups of regions</option>
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125 <option value="no">No, I used only one group</option>
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126 </param>
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127 <when value="no">
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128 <conditional name="clustering">
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129 <param name="clustering_options" type="select" label="Clustering algorithm">
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130 <option value="none">No clustering</option>
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131 <option value="kmeans">Kmeans clustering</option>
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132 <option value="hclust">Hierarchical clustering</option>
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133 </param>
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134 <when value="kmeans">
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135 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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136 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
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137 This only works for data that is not grouped, otherwise only the first group will be clustered.
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138 If more specific clustering methods are required it is advisable to save the underlying matrix and
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139 run the clustering using other software."/>
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140 </when>
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141 <when value="hclust">
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142 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
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143 help="WARNING: This option causes the tool to run for a very long time! When this option is
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144 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
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145 This only works for data that is not grouped, otherwise only the first group will be clustered.
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146 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
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147 If more specific clustering methods are required it is advisable to save the underlying matrix and
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148 run the clustering using other software."/>
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149 </when>
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150 <when value="none" />
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151 </conditional>
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152 </when>
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153 <when value="yes" />
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154 </conditional>
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155 </xml>
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156
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157 <token name="@KMEANS_CLUSTERING@">
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158 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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159 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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160 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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161 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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162 #end if
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163 #end if
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164 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
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165 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
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166 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
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167 #end if
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168 #end if
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169 #end if
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170 </token>
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171
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172 <xml name="samFlags">
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173 <param argument="--samFlagInclude" type="integer" optional="True" value=""
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174 label="Include reads based on the SAM flag"
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175 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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176 <param argument="--samFlagExclude" type="integer" optional="True" value=""
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177 label="Exclude reads based on the SAM flag"
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178 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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179 </xml>
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180
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181 <xml name="fragLength">
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182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
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183 label="Minimum fragment length for inclusion."
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184 help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
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185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
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186 label="Maximum fragment length for inclusion."
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187 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
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188 </xml>
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189
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190 <xml name="read_processing_options">
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191 <expand macro="extendReads" />
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192 <expand macro="ignoreDuplicates" />
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193 <expand macro="centerReads" />
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194 <expand macro="minMappingQuality" />
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195 <expand macro="samFlags" />
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196 <expand macro="fragLength" />
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197 </xml>
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198
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199 <xml name="gtf_options">
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200 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
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201 label="Use a metagene model"
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202 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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203 <param argument="--transcriptID" optional="True" value="transcript" type="text"
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204 label="trascript designator"
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205 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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206 <param argument="--exonID" optional="True" value="exon" type="text"
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207 label="exon designator"
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208 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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209 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
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210 label="transcriptID key designator"
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211 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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212 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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213 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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214 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
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215 </xml>
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216
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217
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218 <xml name="plotNumbers">
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219 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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220 label="Plot the correlation value"
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221 help="If set, then the correlation number is plotted on top of the heatmap."/>
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222 </xml>
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223
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224 <xml name="extendReads">
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225 <conditional name="doExtendCustom">
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226 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
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227 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
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228 By default *each* read mate is extended.
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229 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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230 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
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231 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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232 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
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233 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
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234 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
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235 <option value="custom">A custom length, which will be applied to ALL reads.</option>
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236 </param>
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237 <when value="no" />
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238 <when value="yes" />
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239 <when value="custom">
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240 <param name="extendReadsValue" type="integer" value="300" min="1"
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241 label="Extend reads to the given average fragment size"
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242 help="Extend all reads to this length" />
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243 </when>
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244 </conditional>
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245 </xml>
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246
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247 <xml name="corMethod">
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248 <param argument="--corMethod" type="select" label="Correlation method">
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249 <option value="spearman" selected="True">Spearman</option>
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250 <option value="pearson">Pearson</option>
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251 </param>
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252 </xml>
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253
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254 <xml name="distanceBetweenBins">
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255 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
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256 label="Distance between bins"
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257 help="By default, multiBamSummary considers consecutive bins of
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258 the specified 'Bin size'. However, to reduce the
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259 computation time, a larger distance between bins can
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260 be given. Larger distances result in fewer bins being
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261 considered."/>
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262 </xml>
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263
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264 <xml name="centerReads">
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265 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
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266 label="Center regions with respect to the fragment length"
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267 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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268 </xml>
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269
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270 <xml name="ignoreDuplicates">
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271 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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272 label="Ignore duplicates"
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273 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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274 </xml>
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275
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276 <xml name="sortUsing">
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277 <param argument="--sortUsing" type="select" label="Method used for sorting"
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278 help="For each row the method is computed.">
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279 <option value="mean" selected="true">mean</option>
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280 <option value="median">median</option>
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281 <option value="min">min</option>
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282 <option value="max">max</option>
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283 <option value="sum">sum</option>
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284 <option value="region_length">region length</option>
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285 </param>
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286 </xml>
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287
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288 <xml name="sortRegionsComputeMatrix">
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289 <param argument="--sortRegions" type="select" label="Sort regions"
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290 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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291 <option value="no">no ordering</option>
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292 <option value="keep" selected="true">maintain the same ordering as the input files</option>
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293 <option value="descend">descending order</option>
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294 <option value="ascend">ascending order</option>
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295 </param>
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296 </xml>
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297
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298 <xml name="sortRegions">
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299 <param argument="--sortRegions" type="select" label="Sort regions"
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300 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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301 <option value="no">no ordering</option>
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302 <option value="descend">descending order</option>
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303 <option value="ascend">ascending order</option>
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304 </param>
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305 </xml>
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306
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307 <xml name="minMappingQuality">
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308 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
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309 label="Minimum mapping quality"
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310 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
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311 </xml>
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312
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313 <xml name="skipZeros">
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314 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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315 label ="Skip zeros"
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316 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />
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317 </xml>
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318
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319 <xml name="fragmentLength">
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320 <param argument="--fragmentLength" type="integer" value="300" min="1"
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321 label="Fragment length used for the sequencing"
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322 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
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323 </xml>
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324
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325 <xml name="scaleFactor">
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326 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
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327 help="When used in combination with --normalizeTo1x or
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328 --normalizeUsingRPKM, the computed scaling factor will
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329 be multiplied by the given scale factor." />
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330 </xml>
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331
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332 <xml name="scaleFactors">
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333 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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334 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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335 </xml>
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336
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337 <xml name="stdio">
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338 <stdio>
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339 <exit_code range="1:" />
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340 <exit_code range=":-1" />
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341 <regex match="Error:" />
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342 <regex match="Exception:" />
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343 <regex match="EXception:" />
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344 <regex match="Traceback" />
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345 </stdio>
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346 </xml>
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347
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348 <xml name="pseudocount">
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349 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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350 </xml>
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351
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352 <token name="@REFERENCES@">
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353
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354 .. class:: infomark
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355
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356 For more information on the tools, please visit our `help site`_.
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357
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358 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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359
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360 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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361
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362 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
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363 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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364 .. _help site: https://deeptools.readthedocs.org/
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365
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366 </token>
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367 <xml name="citations">
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368 <citations>
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369 <citation type="doi">10.1093/nar/gkw257</citation>
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370 <yield />
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371 </citations>
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372 </xml>
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373
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374 <xml name="multiple_input_bams">
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375 <conditional name="multibam_conditional">
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376 <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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377 <option value="No" selected="true">No</option>
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378 <option value="Yes">Yes</option>
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379 </param>
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380 <when value="No">
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381 <param argument="--bamfiles" type="data" format="bam" min="1"
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382 label="Bam file" multiple="true"
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383 help=""/>
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384 </when>
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385 <when value="Yes">
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386 <repeat name="multibam_repeats" min="1" title="BAM Files">
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387 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
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388 </repeat>
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389 </when>
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390 </conditional>
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391 </xml>
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392
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393 <xml name="multiple_input_bams_min2">
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394 <conditional name="multibam_conditional">
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395 <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
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396 is vital to you, select Yes below.">
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397 <option value="No" selected="true">No</option>
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398 <option value="Yes">Yes</option>
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399 </param>
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400 <when value="No">
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401 <param argument="--bamfiles" type="data" format="bam" min="2"
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402 label="Bam file" multiple="true"
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403 help=""/>
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404 </when>
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405 <when value="Yes">
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406 <repeat name="multibam_repeats" min="2" title="BAM Files">
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407 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
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408 </repeat>
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409 </when>
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410 </conditional>
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411 </xml>
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412
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413 <xml name="multiple_input_bigwigs">
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414 <conditional name="multibigwig_conditional">
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415 <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
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416 is vital to you, select Yes below.">
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417 <option value="No" selected="true">No</option>
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418 <option value="Yes">Yes</option>
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419 </param>
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420 <when value="No">
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421 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
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422 label="Bigwig file"
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423 help="A Bigwig file."/>
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424 </when>
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425 <when value="Yes">
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426 <repeat name="multibigwig_repeats" min="2" title="BigWig files">
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427 <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
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428 </repeat>
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429 </when>
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430 </conditional>
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431 </xml>
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432
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433 <xml name="plotTitle">
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434 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
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435 label="Title of the plot"
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436 help="Title of the plot, to be printed on top of the generated image." />
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437 </xml>
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438
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439
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440 <token name="@multiple_input_bams@">
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441 <![CDATA[
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442 #set files=[]
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443 #set labels=[]
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444 #if $multibam_conditional.orderMatters == "No":
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445 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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446 ln -s "${bamfile}" "./${counter}.bam" &&
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
448 #silent $files.append('%s.bam' % $counter)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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449 #silent $labels.append("'%s'" % ($bamfile.display_name))
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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450 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
451 #else:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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453 ln -s "${f.bamfile}" "./${counter}.bam" &&
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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454 ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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455 #silent $files.append('%s.bam' % $counter)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
456 #silent $labels.append("'%s'" % ($f.bamfile.display_name))
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
457 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
458 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
459 ]]>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
460 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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461
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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462 <token name="@multiple_input_bigwigs@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
463 <![CDATA[
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
464 #set files=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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465 #set labels=[]
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466 #if $multibigwig_conditional.orderMatters == "No":
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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467 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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468 ln -s "${bigwig}" "${counter}.bw" &&
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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469 #silent $files.append('%s.bw' % $counter)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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470 #silent $labels.append("'%s'" % ($bigwig.display_name))
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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471 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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472 #else:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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473 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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474 ln -s "${f.bigwig}" "${counter}.bw" &&
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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475 #silent $files.append('%s.bw' % $counter)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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476 #silent $labels.append("'%s'" % ($f.bigwig.display_name))
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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477 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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478 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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479 ]]>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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480 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
481
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
482 <xml name="blacklist">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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483 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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484 label="Blacklisted regions in BED/GTF format"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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485 help="One or more files containing regions to exclude from the analysis" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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486 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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487
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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488 <token name="@blacklist@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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489 <![CDATA[
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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490 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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491 #set blfiles=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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492 #for $f in $advancedOpt.blackListFileName:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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493 #silent $blfiles.append("'%s'" % $f)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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494 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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495 #if $blfiles != ["'None'"]:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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496 --blackListFileName #echo ' '.join($blfiles)#
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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497 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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498 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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499 ]]>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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500 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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501
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
502 <xml name="multiple_bed">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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503 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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504 label="Regions in BED/GTF format"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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505 help="One or more files containing regions to include in the analysis" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
506 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
507
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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508 <token name="@multiple_bed@">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
509 <![CDATA[
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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510 #set files=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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511 #set labels=[]
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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512 #for $f in $BED:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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513 #silent $files.append("'%s'" % $f)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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514 #silent $labels.append("'%s'" % $f.display_name)
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
515 #end for
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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516 #if len($files) > 0:
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
517 --BED #echo ' '.join($files)#
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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518 --regionLabels #echo ' '.join($labels)#
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
519 #end if
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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520 ]]>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
521 </token>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
522
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
523 <xml name="reference_genome_source">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
524 <conditional name="source">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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525 <param name="ref_source" type="select" label="Reference genome">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
526 <option value="cached">locally cached</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
527 <option value="history">in your history</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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528 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
529 <when value="cached">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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530 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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531 <options from_data_table="lastz_seqs">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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532 <filter type="sort_by" column="1" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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533 <validator type="no_options" message="No indexes are available." />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
534 </options>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
535 </param>
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536 </when>
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537 <when value="history">
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538 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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539 </when>
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540 </conditional>
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diff changeset
541 </xml>
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542
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diff changeset
543 <token name="@reference_genome_source@">
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544 #if $source.ref_source=="history":
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545 --genome $source.input1
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546 #else:
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diff changeset
547 --genome "$source.input1_2bit.fields.path"
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548 #end if
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549 </token>
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diff changeset
550
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diff changeset
551 <xml name="effectiveGenomeSize">
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552 <conditional name="effectiveGenomeSize">
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diff changeset
553 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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554 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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diff changeset
555 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
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556 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
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diff changeset
557 <option value="93260000">ce10 (93260000)</option>
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558 <option value="121400000">dm3 (121400000)</option>
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559 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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560 <option value="2150570000">mm9 (2150570000)</option>
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561 <option value="specific">user specified</option>
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562 </param>
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diff changeset
563 <when value="specific">
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564 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
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565 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
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diff changeset
566 </when>
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567 <when value="2150570000" />
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568 <when value="2451960000" />
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569 <when value="121400000" />
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570 <when value="93260000" />
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571 </conditional>
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572 </xml>
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573
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574 <xml name="skipNAs">
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575 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
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576 label="Ignore missing data?"
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577 help="This parameter determines if non-covered regions
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578 (regions without overlapping reads) in a bam/bigWig file
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579 should be skipped. The default is to treat those
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580 regions as having a value of zero. The decision to
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581 skip non-covered regions depends on the interpretation
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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582 of the data. Non-covered regions may represent, for
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583 example, repetitive regions that should be ignored.
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584 (default: False)" />
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585 </xml>
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586
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587 <xml name="input_save_matrix_values">
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588 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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589 </xml>
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590
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591 <xml name="input_graphic_output_settings">
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592 <conditional name="output" >
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593 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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594 <option value="no" selected="true">no</option>
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595 <option value="yes">yes</option>
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596 </param>
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597 <when value="no" />
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598 <when value="yes">
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599 <yield />
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600 <param name="saveSortedRegions" type="boolean"
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601 label="Save the regions after skipping zeros or min/max threshold values"
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602 help="The order of the regions in the file follows the sorting order selected. This is useful,
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603 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
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604 </when>
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605 </conditional>
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606 </xml>
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607
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608
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609 <xml name="input_image_file_format">
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610 <param argument="--outFileFormat" type="select" label="Image file format">
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611 <option value="png" selected="true">png</option>
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612 <option value="pdf">pdf</option>
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613 <option value="svg">svg</option>
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614 <option value="eps">eps</option>
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615 </param>
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616 </xml>
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617
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618 <xml name="output_dpi">
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619 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
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620 label="Image dpi" help=""/>
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621 </xml>
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622
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623 <xml name="output_image_file_format">
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624 <data format="png" name="outFileName" label="${tool.name} image">
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diff changeset
625 <change_format>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
626 <when input="output.outFileFormat" value="pdf" format="pdf" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
627 <when input="output.outFileFormat" value="svg" format="svg" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
628 <when input="output.outFileFormat" value="eps" format="eps" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
629 </change_format>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
630 </data>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
631 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
632
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
633 <xml name="output_image_file_format_not_nested">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
634 <data format="png" name="outFileName" label="${tool.name} image">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
635 <change_format>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
636 <when input="outFileFormat" value="pdf" format="pdf" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
637 <when input="outFileFormat" value="svg" format="svg" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
638 <when input="outFileFormat" value="eps" format="eps" />
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
639 </change_format>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
640 </data>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
641 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
642
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
643 <xml name="output_save_matrix_values">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
644 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
645 <filter>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
646 ((
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
647 output['showOutputSettings'] == 'yes' and
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
648 output['saveMatrix'] is True
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
649 ))
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
650 </filter>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
651 </data>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
652 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
653
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
654 <xml name="output_graphic_outputs">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
655 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
656 <filter>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
657 ((
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
658 output['showOutputSettings'] == 'yes' and
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
659 output['saveSortedRegions'] is True
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
660 ))
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
661 </filter>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
662 </data>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
663 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
664
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
665 <xml name="colorMap">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
666 <param name="colorMap" type="select" label="Color map to use for the heatmap"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
667 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
668 multiple="true">
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
669 <option value="RdYlBu" selected="true">RdYlBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
670 <option value="Accent">Accent</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
671 <option value="Spectral">Spectral</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
672 <option value="Set1">Set1</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
673 <option value="Set2">Set2</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
674 <option value="Set3">Set3</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
675 <option value="Dark2">Dark2</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
676 <option value="Reds">Reds</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
677 <option value="Oranges">Oranges</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
678 <option value="Greens">Greens</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
679 <option value="Blues">Blues</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
680 <option value="Greys">Greys</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
681 <option value="Purples">Purples</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
682 <option value="Paired">Paired</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
683 <option value="Pastel1">Pastel1</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
684 <option value="Pastel2">Pastel2</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
685 <option value="spring">spring</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
686 <option value="summer">summer</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
diff changeset
687 <option value="autumn">autumn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
688 <option value="winter">winter</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
689 <option value="hot">hot</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
690 <option value="coolwarm">coolwarm</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
691 <option value="cool">cool</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
692 <option value="seismic">seismic</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
693 <option value="terrain">terrain</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
694 <option value="ocean">ocean</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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695 <option value="rainbow">rainbow</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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696 <option value="bone">bone</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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697 <option value="flag">flag</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
698 <option value="prism">prism</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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699 <option value="cubehelix">cubehelix</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
700 <option value="binary">binary</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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701 <option value="pink">pink</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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702 <option value="gray">gray</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
703 <option value="copper">copper</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
704 <option value="BrBG">BrBG</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
705 <option value="BuGn">BuGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
706 <option value="BuPu">BuPu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
707 <option value="GnBu">GnBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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708 <option value="OrRd">OrRd</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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709 <option value="PiYG">PiYG</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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710 <option value="PRGn">PRGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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parents:
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711 <option value="PuOr">PuOr</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
712 <option value="PuRd">PuRd</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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713 <option value="PuBu">PuBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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714 <option value="RdBu">RdBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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diff changeset
715 <option value="RdGy">RdGy</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
716 <option value="RdPu">RdPu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
717 <option value="YlGn">YlGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
718 <option value="PuBuGn">PuBuGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
719 <option value="RdYlGn">RdYlGn</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
720 <option value="YlGnBu">YlGnBu</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
721 <option value="YlOrBr">YlOrBr</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
722 <option value="YlOrRd">YlOrRd</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
723 <option value="gist_gray">gist_gray</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
724 <option value="gist_stern">gist_stern</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
725 <option value="gist_earth">gist_earth</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
726 <option value="gist_yarg">gist_yarg</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
727 <option value="gist_ncar">gist_ncar</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
728 <option value="gist_rainbow">gist_rainbow</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
729 <option value="gist_heat">gist_heat</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
730 <option value="gnuplot">gnuplot</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
731 <option value="gnuplot2">gnuplot2</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
732 <option value="CMRmap">CMRmap</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
733 <option value="bwr">bwr</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
734 <option value="hsv">hsv</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
735 <option value="brg">brg</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
736 <option value="jet">jet</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
737 <option value="afmhot">afmhot</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
738 <option value="Accent_r">Accent reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
739 <option value="Spectral_r">Spectral reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
740 <option value="Set1_r">Set1 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
741 <option value="Set2_r">Set2 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
742 <option value="Set3_r">Set3 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
743 <option value="Dark2_r">Dark2 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
744 <option value="Reds_r">Reds reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
745 <option value="Oranges_r">Oranges reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
746 <option value="Greens_r">Greens reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
747 <option value="Blues_r">Blues reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
748 <option value="Greys_r">Greys reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
749 <option value="Purples_r">Purples reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
750 <option value="Paired_r">Paired reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
751 <option value="Pastel1_r">Pastel1 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
752 <option value="Pastel2_r">Pastel2 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
753 <option value="spring_r">spring reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
754 <option value="summer_r">summer reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
755 <option value="autumn_r">autumn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
756 <option value="winter_r">winter reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
757 <option value="hot_r">hot reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
758 <option value="coolwarm_r">coolwarm reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
759 <option value="cool_r">cool reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
760 <option value="seismic_r">seismic reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
761 <option value="terrain_r">terrain reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
762 <option value="ocean_r">ocean reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
763 <option value="rainbow_r">rainbow reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
764 <option value="bone_r">bone reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
765 <option value="flag_r">flag reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
766 <option value="prism_r">prism reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
767 <option value="cubehelix_r">cubehelix reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
768 <option value="binary_r">binary reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
769 <option value="pink_r">pink reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
770 <option value="gray_r">gray reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
771 <option value="copper_r">copper reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
772 <option value="BrBG_r">BrBG reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
773 <option value="BuGn_r">BuGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
774 <option value="BuPu_r">BuPu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
775 <option value="GnBu_r">GnBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
776 <option value="OrRd_r">OrRd reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
777 <option value="PiYG_r">PiYG reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
778 <option value="PRGn_r">PRGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
779 <option value="PuOr_r">PuOr reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
780 <option value="PuRd_r">PuRd reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
781 <option value="PuBu_r">PuBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
782 <option value="RdBu_r">RdBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
783 <option value="RdGy_r">RdGy reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
784 <option value="RdPu_r">RdPu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
785 <option value="YlGn_r">YlGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
786 <option value="PuBuGn_r">PuBuGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
787 <option value="RdYlBu_r">RdYlBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
788 <option value="RdYlGn_r">RdYlGn reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
789 <option value="YlGnBu_r">YlGnBu reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
790 <option value="YlOrBr_r">YlOrBr reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
791 <option value="YlOrRd_r">YlOrRd reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
792 <option value="gist_gray_r">gist_gray reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
793 <option value="gist_stern_r">gist_stern reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
794 <option value="gist_earth_r">gist_earth reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
795 <option value="gist_yarg_r">gist_yarg reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
796 <option value="gist_ncar_r">gist_ncar reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
797 <option value="gist_rainbow_r">gist_rainbow reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
798 <option value="gist_heat_r">gist_heat reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
799 <option value="gnuplot_r">gnuplot reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
800 <option value="gnuplot2_r">gnuplot2 reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
801 <option value="CMRmap_r">CMRmap reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
802 <option value="bwr_r">bwr reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
803 <option value="hsv_r">hsv reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
804 <option value="brg_r">brg reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
805 <option value="jet_r">jet reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
806 <option value="afmhot_r">afmhot reversed</option>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
807 </param>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
808
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
809 </xml>
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
810
1638c02b28b5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents:
diff changeset
811 </macros>