Mercurial > repos > bgruening > deeptools_compute_matrix

annotate deepTools_macros.xml @ 9:4b3adcb7c7e9 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2f53e1ab939f99201f72ef1a900cb9c542e3f484
author bgruening
date Tue, 25 Oct 2016 19:32:40 -0400
parents aee77c22123d
children 6f334c8bd52f
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1 <macros>
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2
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3 <xml name="advancedOpt_scaffold">
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4 <conditional name="advancedOpt">
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5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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6 <option value="no" selected="true">no</option>
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7 <option value="yes">yes</option>
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8 </param>
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9 <when value="no" />
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10 <when value="yes">
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11 <yield/>
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12 </when>
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13 </conditional>
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14 </xml>
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15
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16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
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17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
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18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
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19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
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20 --extendReads
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21 #end if
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22 $advancedOpt.ignoreDuplicates
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23 $advancedOpt.centerReads
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24 #if $advancedOpt.minMappingQuality:
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25 --minMappingQuality '$advancedOpt.minMappingQuality'
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26 #end if
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27 #if $advancedOpt.samFlagInclude:
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28 --samFlagInclude $advancedOpt.samFlagInclude
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29 #end if
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30 #if $advancedOpt.samFlagExclude:
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31 --samFlagExclude $advancedOpt.samFlagExclude
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32 #end if
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33 #if $advancedOpt.minFragmentLength:
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34 --minFragmentLength $advancedOpt.minFragmentLength
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35 #end if
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36 #if $advancedOpt.maxFragmentLength:
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37 --maxFragmentLength $advancedOpt.maxFragmentLength
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38 #end if
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39 </token>
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40
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41 <token name="@ADVANCED_OPTS_GTF@">
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42 $advancedOpt.metagene
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43 #if $advancedOpt.transcriptID:
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44 --transcriptID $advancedOpt.transcriptID
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45 #end if
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46 #if $advancedOpt.exonID:
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47 --exonID $advancedOpt.exonID
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48 #end if
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49 #if $advancedOpt.transcript_id_designator:
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50 --transcript_id_designator $advancedOpt.transcript_id_designator
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51 #end if
0
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52 </token>
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53
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54 <xml name="heatmap_options">
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55 <expand macro="zMin_zMax" />
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56 <expand macro="colorMap" />
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57 <expand macro="plotTitle" />
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58 <expand macro="plotNumbers" />
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59 </xml>
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60
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61 <token name="@HEATMAP_OPTIONS@">
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62 #if str($plotting_type.zMin) != "":
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63 --zMin $plotting_type.zMin
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64 #end if
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65 #if str($plotting_type.zMax) != "":
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66 --zMax $plotting_type.zMax
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67 #end if
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68 --colorMap '$plotting_type.colorMap'
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69 $plotting_type.plotNumbers
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70 --plotTitle '$plotting_type.plotTitle'
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71 </token>
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72
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73
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74 <xml name="includeZeros">
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75 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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76 label="Include zeros"
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77 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
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78 </xml>
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79
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80 <xml name="zMin_zMax">
8
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81 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0
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82 help="If not specified the value is set automatically."/>
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83 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0
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84 help="If not specified the value is set automatically."/>
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85 </xml>
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86
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87 <xml name="region_limit_operation">
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88 <param argument="--region" type="text" value=""
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89 label="Region of the genome to limit the operation to"
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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="|"/>
8
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94 <add value=":"/>
6
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95 </valid>
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96 </sanitizer>
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97 </param>
0
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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@">2.3.6</token>
0
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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="2.3.6">deepTools</requirement>
0
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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>
1
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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>
0
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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
1
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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
0
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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
0
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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" />
0
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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="sortRegions">
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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="descend" selected="true">descending order</option>
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293 <option value="ascend">ascending order</option>
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294 </param>
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295 </xml>
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296
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297 <xml name="minMappingQuality">
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298 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0
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299 label="Minimum mapping quality"
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300 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
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301 </xml>
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302
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303 <xml name="skipZeros">
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304 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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305 label ="Skip zeros"
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306 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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307 </xml>
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308
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309 <xml name="fragmentLength">
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310 <param argument="--fragmentLength" type="integer" value="300" min="1"
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311 label="Fragment length used for the sequencing"
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312 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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313 </xml>
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314
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315 <xml name="scaleFactor">
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316 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
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317 help="When used in combination with --normalizeTo1x or
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318 --normalizeUsingRPKM, the computed scaling factor will
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319 be multiplied by the given scale factor." />
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320 </xml>
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321
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322 <xml name="scaleFactors">
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323 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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324 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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325 </xml>
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326
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327 <xml name="stdio">
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328 <stdio>
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329 <exit_code range="1:" />
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330 <exit_code range=":-1" />
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331 <regex match="Error:" />
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332 <regex match="Exception:" />
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333 <regex match="EXception:" />
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334 <regex match="Traceback" />
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335 </stdio>
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336 </xml>
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337
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338 <xml name="pseudocount">
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339 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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340 </xml>
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341
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342 <token name="@REFERENCES@">
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343
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344 .. class:: infomark
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345
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346 For more information on the tools, please visit our `help site`_.
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347
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348 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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349
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350 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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351
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352 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
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353 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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354 .. _help site: https://deeptools.readthedocs.org/
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355
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356 </token>
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357 <xml name="citations">
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358 <citations>
6
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359 <citation type="doi">10.1093/nar/gkw257</citation>
0
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360 <yield />
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361 </citations>
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362 </xml>
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363
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364 <xml name="multiple_input_bams">
1
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365 <param argument="--bamfiles" type="data" format="bam" min="1"
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366 label="Bam file" multiple="true"
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367 help=""/>
1
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368 </xml>
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369
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370 <xml name="multiple_input_bams_min2">
0
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371 <param argument="--bamfiles" type="data" format="bam" min="2"
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372 label="Bam file" multiple="true"
3
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373 help=""/>
0
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374 </xml>
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375
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376 <xml name="multiple_input_bigwigs">
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377 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
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378 label="Bigwig file"
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379 help="A Bigwig file."/>
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380 </xml>
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381
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382 <xml name="plotTitle">
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383 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
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384 label="Title of the plot"
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385 help="Title of the plot, to be printed on top of the generated image." />
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386 </xml>
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387
1
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388
0
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389 <token name="@multiple_input_bams@">
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390 <![CDATA[
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391 #set files=[]
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392 #set labels=[]
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393 #for $counter, $bamfile in enumerate($bamfiles):
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394 ln -s "${bamfile}" "./${counter}.bam" &&
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395 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
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396 #silent $files.append('%s.bam' % $counter)
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397 #silent $labels.append("'%s'" % ($bamfile.display_name))
0
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398 #end for
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399 ]]>
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400 </token>
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401
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402 <token name="@multiple_input_bigwigs@">
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403 <![CDATA[
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404 #set files=[]
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405 #set labels=[]
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406 #for $counter, $bigwig in enumerate($bigwigfiles):
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407 ln -s "${bigwig}" "${counter}.bw" &&
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408 #silent $files.append('%s.bw' % $counter)
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409 #silent $labels.append("'%s'" % ($bigwig.display_name))
0
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410 #end for
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411 ]]>
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412 </token>
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413
8
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414 <xml name="blacklist">
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415 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
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416 label="Blacklisted regions in BED/GTF format"
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417 help="One or more files containing regions to exclude from the analysis" />
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418 </xml>
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419
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420 <token name="@blacklist@">
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421 <![CDATA[
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422 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
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423 #set blfiles=[]
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424 #for $f in $advancedOpt.blackListFileName:
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425 #silent $blfiles.append("'%s'" % $f)
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426 #end for
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427 #if $blfiles != ["'None'"]:
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428 --blackListFileName #echo ' '.join($blfiles)#
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429 #end if
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430 #end if
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431 ]]>
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432 </token>
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433
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434 <xml name="multiple_bed">
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435 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
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436 label="Regions in BED/GTF format"
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437 help="One or more files containing regions to include in the analysis" />
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438 </xml>
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439
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440 <token name="@multiple_bed@">
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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 #for $f in $BED:
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445 #silent $files.append("'%s'" % $f)
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446 #silent $labels.append("'%s'" % $f.display_name)
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447 #end for
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448 #if len($files) > 0:
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449 --BED #echo ' '.join($files)#
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450 --regionLabels #echo ' '.join($labels)#
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451 #end if
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452 ]]>
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453 </token>
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454
0
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455 <xml name="reference_genome_source">
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456 <conditional name="source">
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457 <param name="ref_source" type="select" label="Reference genome">
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458 <option value="cached">locally cached</option>
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459 <option value="history">in your history</option>
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460 </param>
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461 <when value="cached">
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462 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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463 <options from_data_table="lastz_seqs">
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464 <filter type="sort_by" column="1" />
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465 <validator type="no_options" message="No indexes are available." />
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466 </options>
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467 </param>
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468 </when>
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469 <when value="history">
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470 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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471 </when>
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472 </conditional>
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473 </xml>
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474
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475 <token name="@reference_genome_source@">
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476 #if $source.ref_source=="history":
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477 --genome $source.input1
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478 #else:
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479 --genome "$source.input1_2bit.fields.path"
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480 #end if
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481 </token>
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482
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483 <xml name="effectiveGenomeSize">
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484 <conditional name="effectiveGenomeSize">
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485 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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486 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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487 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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488 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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489 <option value="93260000">ce10 (93260000)</option>
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490 <option value="121400000">dm3 (121400000)</option>
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491 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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492 <option value="2150570000">mm9 (2150570000)</option>
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493 <option value="specific">user specified</option>
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494 </param>
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495 <when value="specific">
8
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496 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
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497 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
0
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498 </when>
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499 <when value="2150570000" />
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500 <when value="2451960000" />
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501 <when value="121400000" />
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502 <when value="93260000" />
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503 </conditional>
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504 </xml>
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505
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506 <xml name="skipNAs">
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507 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
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508 label="Ignore missing data?"
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509 help="This parameter determines if non-covered regions
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510 (regions without overlapping reads) in a bam/bigWig file
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511 should be skipped. The default is to treat those
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512 regions as having a value of zero. The decision to
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513 skip non-covered regions depends on the interpretation
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514 of the data. Non-covered regions may represent, for
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515 example, repetitive regions that should be ignored.
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516 (default: False)" />
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517 </xml>
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518
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519 <xml name="input_save_matrix_values">
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520 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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521 </xml>
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522
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523 <xml name="input_graphic_output_settings">
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524 <conditional name="output" >
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525 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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526 <option value="no" selected="true">no</option>
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527 <option value="yes">yes</option>
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528 </param>
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529 <when value="no" />
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530 <when value="yes">
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531 <yield />
8
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532 <param name="saveSortedRegions" type="boolean"
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533 label="Save the regions after skipping zeros or min/max threshold values"
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534 help="The order of the regions in the file follows the sorting order selected. This is useful,
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535 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0
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536 </when>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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537 </conditional>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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538 </xml>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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539
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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540
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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541 <xml name="input_image_file_format">
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542 <param argument="--outFileFormat" type="select" label="Image file format">
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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543 <option value="png" selected="true">png</option>
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544 <option value="pdf">pdf</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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545 <option value="svg">svg</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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546 <option value="eps">eps</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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547 </param>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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548 </xml>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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549
8
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550 <xml name="output_dpi">
aee77c22123d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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551 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
aee77c22123d planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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552 label="Image dpi" help=""/>
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553 </xml>
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554
0
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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555 <xml name="output_image_file_format">
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556 <data format="png" name="outFileName" label="${tool.name} image">
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557 <change_format>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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558 <when input="output.outFileFormat" value="pdf" format="pdf" />
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559 <when input="output.outFileFormat" value="svg" format="svg" />
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560 <when input="output.outFileFormat" value="eps" format="eps" />
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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561 </change_format>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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562 </data>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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563 </xml>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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564
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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565 <xml name="output_image_file_format_not_nested">
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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566 <data format="png" name="outFileName" label="${tool.name} image">
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567 <change_format>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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568 <when input="outFileFormat" value="pdf" format="pdf" />
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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569 <when input="outFileFormat" value="svg" format="svg" />
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570 <when input="outFileFormat" value="eps" format="eps" />
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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571 </change_format>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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572 </data>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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573 </xml>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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574
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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575 <xml name="output_save_matrix_values">
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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576 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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577 <filter>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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578 ((
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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579 output['showOutputSettings'] == 'yes' and
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580 output['saveMatrix'] is True
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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581 ))
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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582 </filter>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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583 </data>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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584 </xml>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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585
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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586 <xml name="output_graphic_outputs">
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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587 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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588 <filter>
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589 ((
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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590 output['showOutputSettings'] == 'yes' and
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591 output['saveSortedRegions'] is True
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592 ))
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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593 </filter>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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594 </data>
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595 </xml>
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596
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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597 <xml name="colorMap">
8
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598 <param name="colorMap" type="select" label="Color map to use for the heatmap"
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599 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
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600 multiple="true">
0
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601 <option value="RdYlBu" selected="true">RdYlBu</option>
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602 <option value="Accent">Accent</option>
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603 <option value="Spectral">Spectral</option>
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604 <option value="Set1">Set1</option>
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605 <option value="Set2">Set2</option>
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606 <option value="Set3">Set3</option>
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607 <option value="Dark2">Dark2</option>
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608 <option value="Reds">Reds</option>
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609 <option value="Oranges">Oranges</option>
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610 <option value="Greens">Greens</option>
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611 <option value="Blues">Blues</option>
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612 <option value="Greys">Greys</option>
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613 <option value="Purples">Purples</option>
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614 <option value="Paired">Paired</option>
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615 <option value="Pastel1">Pastel1</option>
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616 <option value="Pastel2">Pastel2</option>
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617 <option value="spring">spring</option>
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618 <option value="summer">summer</option>
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619 <option value="autumn">autumn</option>
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620 <option value="winter">winter</option>
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621 <option value="hot">hot</option>
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622 <option value="coolwarm">coolwarm</option>
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diff changeset
623 <option value="cool">cool</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
624 <option value="seismic">seismic</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
625 <option value="terrain">terrain</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
626 <option value="ocean">ocean</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
627 <option value="rainbow">rainbow</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
628 <option value="bone">bone</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
629 <option value="flag">flag</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
630 <option value="prism">prism</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
631 <option value="cubehelix">cubehelix</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
632 <option value="binary">binary</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
633 <option value="pink">pink</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
634 <option value="gray">gray</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
635 <option value="copper">copper</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
636 <option value="BrBG">BrBG</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
637 <option value="BuGn">BuGn</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
638 <option value="BuPu">BuPu</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
639 <option value="GnBu">GnBu</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
640 <option value="OrRd">OrRd</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
641 <option value="PiYG">PiYG</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
642 <option value="PRGn">PRGn</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
643 <option value="PuOr">PuOr</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
644 <option value="PuRd">PuRd</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
645 <option value="PuBu">PuBu</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
646 <option value="RdBu">RdBu</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
647 <option value="RdGy">RdGy</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
648 <option value="RdPu">RdPu</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
649 <option value="YlGn">YlGn</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
650 <option value="PuBuGn">PuBuGn</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
651 <option value="RdYlGn">RdYlGn</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
652 <option value="YlGnBu">YlGnBu</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
653 <option value="YlOrBr">YlOrBr</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
654 <option value="YlOrRd">YlOrRd</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
655 <option value="gist_gray">gist_gray</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
656 <option value="gist_stern">gist_stern</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
657 <option value="gist_earth">gist_earth</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
658 <option value="gist_yarg">gist_yarg</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
659 <option value="gist_ncar">gist_ncar</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
660 <option value="gist_rainbow">gist_rainbow</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
661 <option value="gist_heat">gist_heat</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
662 <option value="gnuplot">gnuplot</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
663 <option value="gnuplot2">gnuplot2</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
664 <option value="CMRmap">CMRmap</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
665 <option value="bwr">bwr</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
666 <option value="hsv">hsv</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
667 <option value="brg">brg</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
668 <option value="jet">jet</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
669 <option value="afmhot">afmhot</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
670 <option value="Accent_r">Accent reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
671 <option value="Spectral_r">Spectral reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
672 <option value="Set1_r">Set1 reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
673 <option value="Set2_r">Set2 reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
674 <option value="Set3_r">Set3 reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
675 <option value="Dark2_r">Dark2 reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
676 <option value="Reds_r">Reds reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
677 <option value="Oranges_r">Oranges reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
678 <option value="Greens_r">Greens reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
679 <option value="Blues_r">Blues reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
680 <option value="Greys_r">Greys reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
681 <option value="Purples_r">Purples reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
682 <option value="Paired_r">Paired reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
683 <option value="Pastel1_r">Pastel1 reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
684 <option value="Pastel2_r">Pastel2 reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
685 <option value="spring_r">spring reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
686 <option value="summer_r">summer reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
687 <option value="autumn_r">autumn reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
688 <option value="winter_r">winter reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
689 <option value="hot_r">hot reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
690 <option value="coolwarm_r">coolwarm reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
691 <option value="cool_r">cool reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
692 <option value="seismic_r">seismic reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
693 <option value="terrain_r">terrain reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
694 <option value="ocean_r">ocean reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
695 <option value="rainbow_r">rainbow reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
696 <option value="bone_r">bone reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
697 <option value="flag_r">flag reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
698 <option value="prism_r">prism reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
699 <option value="cubehelix_r">cubehelix reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
700 <option value="binary_r">binary reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
701 <option value="pink_r">pink reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
702 <option value="gray_r">gray reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
703 <option value="copper_r">copper reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
704 <option value="BrBG_r">BrBG reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
705 <option value="BuGn_r">BuGn reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
706 <option value="BuPu_r">BuPu reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
707 <option value="GnBu_r">GnBu reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
708 <option value="OrRd_r">OrRd reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
709 <option value="PiYG_r">PiYG reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
710 <option value="PRGn_r">PRGn reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
711 <option value="PuOr_r">PuOr reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
712 <option value="PuRd_r">PuRd reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
713 <option value="PuBu_r">PuBu reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
714 <option value="RdBu_r">RdBu reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
715 <option value="RdGy_r">RdGy reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
716 <option value="RdPu_r">RdPu reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
717 <option value="YlGn_r">YlGn reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
718 <option value="PuBuGn_r">PuBuGn reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
719 <option value="RdYlBu_r">RdYlBu reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
720 <option value="RdYlGn_r">RdYlGn reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
721 <option value="YlGnBu_r">YlGnBu reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
722 <option value="YlOrBr_r">YlOrBr reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
723 <option value="YlOrRd_r">YlOrRd reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
724 <option value="gist_gray_r">gist_gray reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
725 <option value="gist_stern_r">gist_stern reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
726 <option value="gist_earth_r">gist_earth reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
727 <option value="gist_yarg_r">gist_yarg reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
728 <option value="gist_ncar_r">gist_ncar reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
729 <option value="gist_rainbow_r">gist_rainbow reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
730 <option value="gist_heat_r">gist_heat reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
731 <option value="gnuplot_r">gnuplot reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
732 <option value="gnuplot2_r">gnuplot2 reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
733 <option value="CMRmap_r">CMRmap reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
734 <option value="bwr_r">bwr reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
735 <option value="hsv_r">hsv reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
736 <option value="brg_r">brg reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
737 <option value="jet_r">jet reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
738 <option value="afmhot_r">afmhot reversed</option>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
739 </param>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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parents:
diff changeset
740
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
741 </xml>
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
742
14cb57237e46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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743 </macros>