Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

annotate deepTools_macros.xml @ 29:195e98217334 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 14:31:58 +0000
parents 7c1beb6d6eca
children c06951d10364
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1 <macros>
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3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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4 <token name="@TOOL_VERSION@">3.5.2</token>
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5 <token name="@GALAXY_VERSION@">20.01</token>
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6 <xml name="requirements">
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
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9 <requirement type="package" version="1.9">samtools</requirement>
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10 </requirements>
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11 <expand macro="stdio" />
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12 <version_command>@BINARY@ --version</version_command>
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13 </xml>
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14
0
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15 <xml name="advancedOpt_scaffold">
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16 <conditional name="advancedOpt">
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17 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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18 <option value="no" selected="true">no</option>
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19 <option value="yes">yes</option>
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20 </param>
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21 <when value="no" />
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22 <when value="yes">
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23 <yield/>
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24 </when>
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25 </conditional>
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26 </xml>
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28 <token name="@PLOTWIDTHHEIGHT@">
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29 --plotWidth '$advancedOpt.plotWidth'
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30 --plotHeight '$advancedOpt.plotHeight'
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31 </token>
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33 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
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34 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
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35 label="Plot height"
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36 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
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38 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
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39 label="Plot width"
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40 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
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41 </xml>
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42
0
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43 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
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44 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
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45 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
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46 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
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47 --extendReads
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48 #end if
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49 $advancedOpt.ignoreDuplicates
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50 $advancedOpt.centerReads
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51 #if $advancedOpt.minMappingQuality:
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52 --minMappingQuality '$advancedOpt.minMappingQuality'
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53 #end if
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54 #if $advancedOpt.samFlagInclude:
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55 --samFlagInclude $advancedOpt.samFlagInclude
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56 #end if
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57 #if $advancedOpt.samFlagExclude:
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58 --samFlagExclude $advancedOpt.samFlagExclude
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59 #end if
8
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60 #if $advancedOpt.minFragmentLength:
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61 --minFragmentLength $advancedOpt.minFragmentLength
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62 #end if
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63 #if $advancedOpt.maxFragmentLength:
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64 --maxFragmentLength $advancedOpt.maxFragmentLength
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65 #end if
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66 </token>
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67
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68 <token name="@ADVANCED_OPTS_GTF@">
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69 $advancedOpt.metagene
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70 #if $advancedOpt.transcriptID:
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71 --transcriptID $advancedOpt.transcriptID
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72 #end if
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73 #if $advancedOpt.exonID:
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74 --exonID $advancedOpt.exonID
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75 #end if
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76 #if $advancedOpt.transcript_id_designator:
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77 --transcript_id_designator $advancedOpt.transcript_id_designator
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78 #end if
0
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79 </token>
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80
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81 <xml name="heatmap_options">
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82 <expand macro="zMin_zMax" />
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83 <expand macro="colorMap" />
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84 <expand macro="plotTitle" />
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85 <expand macro="plotNumbers" />
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86 </xml>
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87
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88 <token name="@HEATMAP_OPTIONS@">
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89 #if str($plotting_type.zMin) != "":
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90 --zMin $plotting_type.zMin
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91 #end if
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92 #if str($plotting_type.zMax) != "":
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93 --zMax $plotting_type.zMax
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94 #end if
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95 --colorMap '$plotting_type.colorMap'
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96 $plotting_type.plotNumbers
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97 --plotTitle '$plotting_type.plotTitle'
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98 </token>
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99
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100
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101 <xml name="includeZeros">
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102 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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103 label="Include zeros"
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104 help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />
0
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105 </xml>
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106
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107 <xml name="zMin_zMax">
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108 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0
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109 help="If not specified the value is set automatically."/>
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110 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0
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111 help="If not specified the value is set automatically."/>
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112 </xml>
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113
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114 <xml name="region_limit_operation">
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115 <param argument="--region" type="text" value=""
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116 label="Region of the genome to limit the operation to"
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117 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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118 <sanitizer>
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119 <valid initial="string.letters,string.digits">
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120 <add value="|"/>
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121 <add value=":"/>
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122 <add value="."/>
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123 </valid>
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124 </sanitizer>
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125 </param>
0
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126 </xml>
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127
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128 <xml name="smoothLength">
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129 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
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130 label="Smooth values using the following length (in bases)"
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131 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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132 </xml>
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133
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134
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135 <xml name="kmeans_clustering">
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136 <conditional name="used_multiple_regions">
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137 <param name="used_multiple_regions_options" type="select"
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138 label="Did you compute the matrix with more than one groups of regions?"
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139 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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140 <option value="yes">Yes, I used multiple groups of regions</option>
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141 <option value="no">No, I used only one group</option>
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142 </param>
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143 <when value="no">
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144 <conditional name="clustering">
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145 <param name="clustering_options" type="select" label="Clustering algorithm">
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146 <option value="none">No clustering</option>
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147 <option value="kmeans">Kmeans clustering</option>
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148 <option value="hclust">Hierarchical clustering</option>
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149 </param>
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150 <when value="kmeans">
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151 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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152 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
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153 This only works for data that is not grouped, otherwise only the first group will be clustered.
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154 If more specific clustering methods are required it is advisable to save the underlying matrix and
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155 run the clustering using other software."/>
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156 </when>
1
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157 <when value="hclust">
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158 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
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159 help="WARNING: This option causes the tool to run for a very long time! When this option is
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160 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
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161 This only works for data that is not grouped, otherwise only the first group will be clustered.
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162 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
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163 If more specific clustering methods are required it is advisable to save the underlying matrix and
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164 run the clustering using other software."/>
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165 </when>
0
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166 <when value="none" />
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167 </conditional>
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168 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
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169 label="Compute the silhouette score for each region"
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170 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
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171 The silhouette score is a measure of how similar a region is to other regions in the same cluster as
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172 opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
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173 The silhouette evaluation can be very slow when you have more than 100 000 regions." />
0
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174 </when>
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175 <when value="yes" />
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176 </conditional>
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177 </xml>
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178
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179 <token name="@KMEANS_CLUSTERING@">
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180 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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181 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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182 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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183 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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184 #end if
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185 #end if
1
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186 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
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187 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
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188 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
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189 #end if
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190 #end if
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191 $advancedOpt.used_multiple_regions.silhouette
0
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192 #end if
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193 </token>
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194
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195 <xml name="samFlags">
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196 <param argument="--samFlagInclude" type="integer" optional="True" value=""
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197 label="Include reads based on the SAM flag"
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198 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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199 <param argument="--samFlagExclude" type="integer" optional="True" value=""
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200 label="Exclude reads based on the SAM flag"
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201 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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202 </xml>
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203
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204 <xml name="fragLength">
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205 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
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206 label="Minimum fragment length for inclusion."
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207 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
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208 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
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209 label="Maximum fragment length for inclusion."
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210 help="A value of 0 (the default) is equivalent to no maximum." />
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211 </xml>
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212
0
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213 <xml name="read_processing_options">
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214 <expand macro="extendReads" />
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215 <expand macro="ignoreDuplicates" />
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216 <expand macro="centerReads" />
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217 <expand macro="minMappingQuality" />
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218 <expand macro="samFlags" />
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219 <expand macro="fragLength" />
0
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220 </xml>
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221
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222 <xml name="gtf_options">
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223 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
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224 label="Use a metagene model"
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225 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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226 <param argument="--transcriptID" optional="True" value="transcript" type="text"
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227 label="transcript designator"
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228 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
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229 <param argument="--exonID" optional="True" value="exon" type="text"
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230 label="exon designator"
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231 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
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232 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
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233 label="transcriptID key designator"
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234 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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235 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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236 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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237 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
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238 </xml>
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239
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240
0
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241 <xml name="plotNumbers">
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242 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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243 label="Plot the correlation value"
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244 help="If set, then the correlation number is plotted on top of the heatmap."/>
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245 </xml>
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246
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247 <xml name="extendReads">
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248 <conditional name="doExtendCustom">
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249 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
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250 help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
0
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251 By default *each* read mate is extended.
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252 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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253 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
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254 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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255 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
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256 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
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257 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
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258 <option value="custom">A custom length, which will be applied to ALL reads.</option>
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259 </param>
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260 <when value="no" />
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261 <when value="yes" />
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262 <when value="custom">
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263 <param name="extendReadsValue" type="integer" value="300" min="1"
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264 label="Extend reads to the given average fragment size"
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265 help="Extend all reads to this length" />
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266 </when>
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267 </conditional>
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268 </xml>
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269
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270 <xml name="corMethod">
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271 <param argument="--corMethod" type="select" label="Correlation method">
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272 <option value="spearman" selected="True">Spearman</option>
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273 <option value="pearson">Pearson</option>
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274 </param>
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275 </xml>
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276
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277 <xml name="distanceBetweenBins">
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278 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
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279 label="Distance between bins"
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280 help="By default, multiBamSummary considers consecutive bins of
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281 the specified 'Bin size'. However, to reduce the
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282 computation time, a larger distance between bins can
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283 be given. Larger distances result in fewer bins being
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284 considered."/>
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285 </xml>
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286
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287 <xml name="centerReads">
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288 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
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289 label="Center regions with respect to the fragment length"
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290 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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291 </xml>
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292
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293 <xml name="ignoreDuplicates">
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294 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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295 label="Ignore duplicates"
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296 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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297 </xml>
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298
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299 <xml name="sortUsing">
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300 <param argument="--sortUsing" type="select" label="Method used for sorting"
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301 help="For each row the method is computed.">
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302 <option value="mean" selected="true">mean</option>
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303 <option value="median">median</option>
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304 <option value="min">min</option>
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305 <option value="max">max</option>
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306 <option value="sum">sum</option>
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307 <option value="region_length">region length</option>
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308 </param>
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309 </xml>
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310
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311 <xml name="sortRegionsComputeMatrix">
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312 <param argument="--sortRegions" type="select" label="Sort regions"
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313 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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314 <option value="no">no ordering</option>
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315 <option value="keep" selected="true">maintain the same ordering as the input files</option>
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316 <option value="descend">descending order</option>
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317 <option value="ascend">ascending order</option>
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318 </param>
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319 </xml>
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320
0
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321 <xml name="sortRegions">
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322 <param argument="--sortRegions" type="select" label="Sort regions"
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323 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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324 <option value="no">maintain the same ordering as the input files</option>
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325 <option value="descend" selected="true">descending order</option>
0
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326 <option value="ascend">ascending order</option>
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327 </param>
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328 </xml>
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329
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330 <xml name="minMappingQuality">
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331 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0
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332 label="Minimum mapping quality"
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333 help= "If set, only reads with a mapping quality score at least this high are considered."/>
0
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334 </xml>
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335
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336 <xml name="skipZeros">
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337 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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338 label ="Skip zeros"
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339 help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />
0
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340 </xml>
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341
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342 <xml name="fragmentLength">
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343 <param argument="--fragmentLength" type="integer" min="1" optional="true"
0
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344 label="Fragment length used for the sequencing"
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345 help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/>
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346 </xml>
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347
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348 <xml name="scaleFactor">
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349 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
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350 help="The computed scaling factor will be multiplied by this (default 1)." />
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351 </xml>
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352
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353 <xml name="scaleFactors">
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354 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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355 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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356 </xml>
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357
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358 <xml name="stdio">
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359 <stdio>
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360 <exit_code range="1:" />
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361 <exit_code range=":-1" />
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362 <regex match="Error:" />
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363 <regex match="Exception:" />
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364 <regex match="EXception:" />
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365 <regex match="Traceback" />
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366 </stdio>
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367 </xml>
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368
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369 <xml name="pseudocount">
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370 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
0
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371 </xml>
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372 <token name="@REFERENCES@">
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373
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374 .. class:: infomark
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375
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376 For more information on the tools, please visit our `help site`_.
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377
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378 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
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379
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380 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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381
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382 .. _Biostars: http://biostars.org
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383 .. _on github: http://github.com
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384 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
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385 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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386 .. _help site: https://deeptools.readthedocs.org/
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387
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388 </token>
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389 <xml name="citations">
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390 <citations>
6
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391 <citation type="doi">10.1093/nar/gkw257</citation>
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392 <yield />
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393 </citations>
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394 </xml>
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395
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396 <xml name="multiple_input_bams" tokens="MIN">
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397 <conditional name="multibam_conditional">
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398 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
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399 <option value="No" selected="true">No</option>
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400 <option value="Yes">Yes</option>
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401 </param>
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402 <when value="No">
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403 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
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404 label="BAM/CRAM file" multiple="true"
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405 help=""/>
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406 </when>
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407 <when value="Yes">
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408 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
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409 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
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410 </repeat>
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411 </when>
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412 </conditional>
1
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413 </xml>
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414
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415 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
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416 <conditional name="multibigwig_conditional">
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417 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
10
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418 is vital to you, select Yes below.">
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419 <option value="No" selected="true">No</option>
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420 <option value="Yes">Yes</option>
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421 </param>
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422 <when value="No">
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423 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
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424 label="@LABEL@"
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425 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
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426 </when>
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427 <when value="Yes">
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428 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
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429 <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
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430 </repeat>
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431 </when>
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432 </conditional>
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433 </xml>
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434
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435 <xml name="custom_sample_labels">
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436 <conditional name="custom_sample_labels_conditional">
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437 <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
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438 <option value="No" selected="true">No, use sample names in the history</option>
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439 <option value="Yes">Yes, I want to specify new labels</option>
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440 </param>
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441 <when value="No">
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442 </when>
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443 <when value="Yes">
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444 <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., &quot;sample 1&quot; &quot;sample 2&quot;)">
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445 <sanitizer>
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446 <valid initial="string.printable">
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447 </valid>
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448 </sanitizer>
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449 </param>
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450 </when>
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451 </conditional>
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452 </xml>
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453
0
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454 <xml name="plotTitle">
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455 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
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456 label="Title of the plot"
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457 help="Title of the plot, to be printed on top of the generated image." />
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458 </xml>
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459
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460 <xml name="legendLocation">
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461 <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
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462 <option value="best" selected="true">Best (automatic)</option>
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463 <option value="upper-right">upper-right</option>
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464 <option value="upper-left">upper-left</option>
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465 <option value="upper-center">upper-center</option>
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466 <option value="lower-right">lower-right</option>
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467 <option value="lower-left">lower-left</option>
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468 <option value="lower-center">lower-center</option>
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469 <option value="center-right">center-right</option>
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470 <option value="center-left">center-left</option>
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471 <option value="center">center</option>
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472 <option value="none">none (only works for heatmaps</option>
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473 </param>
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474 </xml>
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475
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476 <xml name="labelRotation">
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477 <param argument="--labelRotation" type="integer" value="0"
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478 label="Rotation of the X-axis labels (in degrees)"
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479 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
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480 </xml>
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481
1
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482
0
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483 <token name="@multiple_input_bams@">
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484 <![CDATA[
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485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
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486 #set custom_labels=$custom_sample_labels_conditional.labels
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487 #end if
0
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488 #set files=[]
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489 #set labels=[]
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490 #import re
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491 #if $multibam_conditional.orderMatters == "No":
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492 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
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493 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
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494 ln -s '${bamfile}' './${counter}.bam' &&
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495 #if $bamfile.ext == 'bam':
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496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
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497 #else:
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498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
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499 #end if
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500 #silent $files.append("'%s.bam'" % $counter)
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501 #silent $labels.append("'%s'" % $identifier)
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502 #end for
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503 #else:
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504 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
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505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
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506 ln -s '${f.bamfiles}' './${counter}.bam' &&
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507 #if $f.bamfiles.ext == 'bam':
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508 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
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509 #else:
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510 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
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511 #end if
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512 #silent $files.append("'%s.bam'" % $counter)
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513 #silent $labels.append("'%s'" % $identifier)
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514 #end for
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515 #end if
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516 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
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517 #set labels=custom_labels
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518 #end if
0
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519 ]]>
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520 </token>
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521
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522 <token name="@multiple_input_bigwigs@">
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523 <![CDATA[
23
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524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
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525 #set custom_labels=$custom_sample_labels_conditional.labels
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526 #end if
0
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527 #set files=[]
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528 #set labels=[]
12
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529 #import re
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530 #if $multibigwig_conditional.orderMatters == "No":
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531 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
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532 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
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533 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
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534 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
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535 #silent $labels.append("'%s'" % $identifier)
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536 #end for
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537 #else:
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538 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
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539 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
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540 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
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541 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
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542 #silent $labels.append("'%s'" % $identifier)
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543 #end for
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544 #end if
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545 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
22
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546 #set labels=custom_labels
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547 #end if
0
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548 ]]>
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549 </token>
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550
8
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551 <xml name="blacklist">
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552 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
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553 label="Blacklisted regions in BED/GTF format"
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554 help="One or more files containing regions to exclude from the analysis" />
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555 </xml>
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556
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557 <token name="@blacklist@">
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558 <![CDATA[
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559 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
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560 #set blfiles=[]
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561 #for $f in $advancedOpt.blackListFileName:
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562 #silent $blfiles.append("'%s'" % $f)
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563 #end for
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diff changeset
564 #if $blfiles != ["'None'"]:
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565 --blackListFileName #echo ' '.join($blfiles)#
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diff changeset
566 #end if
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diff changeset
567 #end if
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parents: 16
diff changeset
568 ]]>
8
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diff changeset
569 </token>
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parents: 7
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570
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diff changeset
571 <xml name="multiple_bed">
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572 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
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573 label="Regions in BED/GTF format"
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574 help="One or more files containing regions to include in the analysis" />
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575 </xml>
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576
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577 <token name="@multiple_bed@">
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578 <![CDATA[
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579 #set files=[]
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580 #set labels=[]
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581 #for $f in $BED:
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582 #silent $files.append("'%s'" % $f)
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583 #silent $labels.append("'%s'" % $f.display_name)
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diff changeset
584 #end for
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585 #if len($files) > 0:
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586 --BED #echo ' '.join($files)#
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587 --regionLabels #echo ' '.join($labels)#
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588 #end if
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589 ]]>
8
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diff changeset
590 </token>
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591
0
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592 <xml name="reference_genome_source">
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593 <conditional name="source">
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594 <param name="ref_source" type="select" label="Reference genome">
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595 <option value="cached">locally cached</option>
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596 <option value="history">in your history</option>
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597 </param>
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598 <when value="cached">
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599 <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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600 <options from_data_table="lastz_seqs">
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601 <filter type="sort_by" column="1" />
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602 <validator type="no_options" message="No indexes are available." />
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603 </options>
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604 </param>
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605 </when>
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606 <when value="history">
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607 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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608 </when>
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609 </conditional>
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610 </xml>
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611
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612 <token name="@reference_genome_source@">
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613 #if $source.ref_source=="history":
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614 --genome $source.input1
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615 #else:
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616 --genome '$source.input1_2bit.fields.path'
0
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617 #end if
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618 </token>
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619
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620 <xml name="effectiveGenomeSize">
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621 <conditional name="effectiveGenomeSize">
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622 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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623 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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624 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
17
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625 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
0
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626 <option value="93260000">ce10 (93260000)</option>
17
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627 <option value="130428560">dm3 (130428560)</option>
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628 <option value="125464728">dm6 (125464728)</option>
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629 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
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630 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
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631 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
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632 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
0
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633 <option value="specific">user specified</option>
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634 </param>
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635 <when value="specific">
8
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636 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
17
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637 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
0
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638 </when>
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639 <when value="93260000" />
17
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640 <when value="130428560" />
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641 <when value="125464728" />
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642 <when value="2685511504" />
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643 <when value="2701495761" />
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644 <when value="2304947926" />
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645 <when value="2308125349" />
0
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646 </conditional>
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647 </xml>
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648
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649 <xml name="skipNAs">
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650 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
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651 label="Ignore missing data?"
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652 help="This parameter determines if non-covered regions
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653 (regions without overlapping reads) in a bam/bigWig file
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654 should be skipped. The default is to treat those
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655 regions as having a value of zero. The decision to
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656 skip non-covered regions depends on the interpretation
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657 of the data. Non-covered regions may represent, for
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658 example, repetitive regions that should be ignored.
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659 (default: False)" />
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660 </xml>
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661
24
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662 <xml name="skipZeroOverZero">
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663 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
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664 help="Skip bins where BOTH files lack coverage.">
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665 <option value="" selected="true">No</option>
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666 <option value="--skipZeroOverZero">Yes, skip them.</option>
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667 </param>
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668 </xml>
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669
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670 <xml name="exactScaling">
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671 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
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672 label="Compute an exact scaling factor"
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673 help="Compute an exact scaling factor rather than one based on
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674 sampled reads. This is only useful in cases where you are
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675 filtering some alignments out AND this are both rare and
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676 tend to clump together in the genome. In such cases the
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677 region-based sampling employed by deepTools would produce
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678 inaccurate scaling factors. Note that this option results
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679 in the process taking significantly more time to complete." />
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680 </xml>
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681
0
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682 <xml name="input_save_matrix_values">
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683 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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684 </xml>
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685
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686 <xml name="input_graphic_output_settings">
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687 <conditional name="output" >
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688 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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689 <option value="no" selected="true">no</option>
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690 <option value="yes">yes</option>
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691 </param>
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692 <when value="no" />
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693 <when value="yes">
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694 <yield />
8
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695 <param name="saveSortedRegions" type="boolean"
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diff changeset
696 argument="--outFileSortedRegions"
8
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697 label="Save the regions after skipping zeros or min/max threshold values"
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698 help="The order of the regions in the file follows the sorting order selected. This is useful,
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diff changeset
699 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0
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700 </when>
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701 </conditional>
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702 </xml>
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diff changeset
703
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diff changeset
704
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705 <xml name="input_image_file_format">
17
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diff changeset
706 <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
0
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707 <option value="png" selected="true">png</option>
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708 <option value="pdf">pdf</option>
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709 <option value="svg">svg</option>
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710 <option value="eps">eps</option>
17
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diff changeset
711 <option value="plotly">plotly</option>
0
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712 </param>
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713 </xml>
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714
8
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diff changeset
715 <xml name="output_dpi">
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diff changeset
716 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
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diff changeset
717 label="Image dpi" help=""/>
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718 </xml>
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diff changeset
719
0
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720 <xml name="output_image_file_format">
21
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diff changeset
721 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0
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diff changeset
722 <change_format>
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723 <when input="output.outFileFormat" value="pdf" format="pdf" />
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diff changeset
724 <when input="output.outFileFormat" value="svg" format="svg" />
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725 <when input="output.outFileFormat" value="eps" format="eps" />
17
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diff changeset
726 <when input="output.outFileFormat" value="plotly" format="html" />
0
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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727 </change_format>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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728 </data>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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diff changeset
729 </xml>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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730
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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diff changeset
731 <xml name="output_image_file_format_not_nested">
21
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diff changeset
732 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0
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diff changeset
733 <change_format>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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734 <when input="outFileFormat" value="pdf" format="pdf" />
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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735 <when input="outFileFormat" value="svg" format="svg" />
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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736 <when input="outFileFormat" value="eps" format="eps" />
17
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diff changeset
737 <when input="outFileFormat" value="plotly" format="html" />
0
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738 </change_format>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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739 </data>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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740 </xml>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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741
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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742 <xml name="output_save_matrix_values">
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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743 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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744 <filter>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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745 ((
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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746 output['showOutputSettings'] == 'yes' and
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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747 output['saveMatrix'] is True
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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748 ))
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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749 </filter>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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750 </data>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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751 </xml>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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752
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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753 <xml name="output_graphic_outputs">
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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754 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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755 <filter>
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756 ((
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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757 output['showOutputSettings'] == 'yes' and
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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758 output['saveSortedRegions'] is True
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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759 ))
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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760 </filter>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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761 </data>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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762 </xml>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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763
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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764 <xml name="colorMap">
8
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diff changeset
765 <param name="colorMap" type="select" label="Color map to use for the heatmap"
17
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766 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
0
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767 <option value="RdYlBu" selected="true">RdYlBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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768 <option value="Accent">Accent</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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769 <option value="Spectral">Spectral</option>
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770 <option value="Set1">Set1</option>
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771 <option value="Set2">Set2</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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772 <option value="Set3">Set3</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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773 <option value="Dark2">Dark2</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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774 <option value="Reds">Reds</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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775 <option value="Oranges">Oranges</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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776 <option value="Greens">Greens</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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777 <option value="Blues">Blues</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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diff changeset
778 <option value="Greys">Greys</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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parents:
diff changeset
779 <option value="Purples">Purples</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
780 <option value="Paired">Paired</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
781 <option value="Pastel1">Pastel1</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
782 <option value="Pastel2">Pastel2</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
783 <option value="spring">spring</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
784 <option value="summer">summer</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
785 <option value="autumn">autumn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
786 <option value="winter">winter</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
787 <option value="hot">hot</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
788 <option value="coolwarm">coolwarm</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
789 <option value="cool">cool</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
790 <option value="seismic">seismic</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
791 <option value="terrain">terrain</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
792 <option value="ocean">ocean</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
793 <option value="rainbow">rainbow</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
794 <option value="bone">bone</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
795 <option value="flag">flag</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
796 <option value="prism">prism</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
797 <option value="cubehelix">cubehelix</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
798 <option value="binary">binary</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
799 <option value="pink">pink</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
800 <option value="gray">gray</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
801 <option value="copper">copper</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
802 <option value="BrBG">BrBG</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
803 <option value="BuGn">BuGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
804 <option value="BuPu">BuPu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
805 <option value="GnBu">GnBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
806 <option value="OrRd">OrRd</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
807 <option value="PiYG">PiYG</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
808 <option value="PRGn">PRGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
809 <option value="PuOr">PuOr</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
810 <option value="PuRd">PuRd</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
811 <option value="PuBu">PuBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
812 <option value="RdBu">RdBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
813 <option value="RdGy">RdGy</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
814 <option value="RdPu">RdPu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
815 <option value="YlGn">YlGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
816 <option value="PuBuGn">PuBuGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
817 <option value="RdYlGn">RdYlGn</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
818 <option value="YlGnBu">YlGnBu</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
819 <option value="YlOrBr">YlOrBr</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
820 <option value="YlOrRd">YlOrRd</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
821 <option value="gist_gray">gist_gray</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
822 <option value="gist_stern">gist_stern</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
823 <option value="gist_earth">gist_earth</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
824 <option value="gist_yarg">gist_yarg</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
825 <option value="gist_ncar">gist_ncar</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
826 <option value="gist_rainbow">gist_rainbow</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
827 <option value="gist_heat">gist_heat</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
828 <option value="gnuplot">gnuplot</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
829 <option value="gnuplot2">gnuplot2</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
830 <option value="CMRmap">CMRmap</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
831 <option value="bwr">bwr</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
832 <option value="hsv">hsv</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
833 <option value="brg">brg</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
834 <option value="jet">jet</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
835 <option value="afmhot">afmhot</option>
26
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
836 <option value="Wistia">Wistia</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
837 <option value="cividis">cividis</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
838 <option value="icefire">icefire</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
839 <option value="inferno">inferno</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
840 <option value="magma">magma</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
841 <option value="mako">mako</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
842 <option value="nipy_spectral">nipy_spectral</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
843 <option value="plasma">plasma</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
844 <option value="rocket">rocket</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
845 <option value="tab10">tab10</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
846 <option value="tab20">tab20</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
847 <option value="tab20b">tab20b</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
848 <option value="tab20c">tab20c</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
849 <option value="twilight">twilight</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
850 <option value="twilight_shifted">twilight_shifted</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
851 <option value="viridis">viridis</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
852 <option value="vlag">vlag</option>
0
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
853 <option value="Accent_r">Accent reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
854 <option value="Spectral_r">Spectral reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
855 <option value="Set1_r">Set1 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
856 <option value="Set2_r">Set2 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
857 <option value="Set3_r">Set3 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
858 <option value="Dark2_r">Dark2 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
859 <option value="Reds_r">Reds reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
860 <option value="Oranges_r">Oranges reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
861 <option value="Greens_r">Greens reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
862 <option value="Blues_r">Blues reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
863 <option value="Greys_r">Greys reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
864 <option value="Purples_r">Purples reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
865 <option value="Paired_r">Paired reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
866 <option value="Pastel1_r">Pastel1 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
867 <option value="Pastel2_r">Pastel2 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
868 <option value="spring_r">spring reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
869 <option value="summer_r">summer reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
870 <option value="autumn_r">autumn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
871 <option value="winter_r">winter reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
872 <option value="hot_r">hot reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
873 <option value="coolwarm_r">coolwarm reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
874 <option value="cool_r">cool reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
875 <option value="seismic_r">seismic reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
876 <option value="terrain_r">terrain reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
877 <option value="ocean_r">ocean reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
878 <option value="rainbow_r">rainbow reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
879 <option value="bone_r">bone reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
880 <option value="flag_r">flag reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
881 <option value="prism_r">prism reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
882 <option value="cubehelix_r">cubehelix reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
883 <option value="binary_r">binary reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
884 <option value="pink_r">pink reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
885 <option value="gray_r">gray reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
886 <option value="copper_r">copper reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
887 <option value="BrBG_r">BrBG reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
888 <option value="BuGn_r">BuGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
889 <option value="BuPu_r">BuPu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
890 <option value="GnBu_r">GnBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
891 <option value="OrRd_r">OrRd reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
892 <option value="PiYG_r">PiYG reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
893 <option value="PRGn_r">PRGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
894 <option value="PuOr_r">PuOr reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
895 <option value="PuRd_r">PuRd reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
896 <option value="PuBu_r">PuBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
897 <option value="RdBu_r">RdBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
898 <option value="RdGy_r">RdGy reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
899 <option value="RdPu_r">RdPu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
900 <option value="YlGn_r">YlGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
901 <option value="PuBuGn_r">PuBuGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
902 <option value="RdYlBu_r">RdYlBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
903 <option value="RdYlGn_r">RdYlGn reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
904 <option value="YlGnBu_r">YlGnBu reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
905 <option value="YlOrBr_r">YlOrBr reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
906 <option value="YlOrRd_r">YlOrRd reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
907 <option value="gist_gray_r">gist_gray reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
908 <option value="gist_stern_r">gist_stern reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
909 <option value="gist_earth_r">gist_earth reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
910 <option value="gist_yarg_r">gist_yarg reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
911 <option value="gist_ncar_r">gist_ncar reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
912 <option value="gist_rainbow_r">gist_rainbow reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
913 <option value="gist_heat_r">gist_heat reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
914 <option value="gnuplot_r">gnuplot reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
915 <option value="gnuplot2_r">gnuplot2 reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
916 <option value="CMRmap_r">CMRmap reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
917 <option value="bwr_r">bwr reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
918 <option value="hsv_r">hsv reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
919 <option value="brg_r">brg reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
920 <option value="jet_r">jet reversed</option>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
921 <option value="afmhot_r">afmhot reversed</option>
26
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
922 <option value="Wistia_r">Wistia reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
923 <option value="cividis_r">cividis reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
924 <option value="icefire_r">icefire reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
925 <option value="inferno_r">inferno reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
926 <option value="magma_r">magma reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
927 <option value="mako_r">mako reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
928 <option value="nipy_spectral_r">nipy_spectral reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
929 <option value="plasma_r">plasma reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
930 <option value="rocket_r">rocket reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
931 <option value="tab10_r">tab10 reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
932 <option value="tab20_r">tab20 reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
933 <option value="tab20b_r">tab20b reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
934 <option value="tab20c_r">tab20c reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
935 <option value="twilight_r">twilight reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
936 <option value="twilight_shifted_r">twilight_shifted reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
937 <option value="viridis_r">viridis reversed</option>
62eb6d63f582 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 25
diff changeset
938 <option value="vlag_r">vlag reversed</option>
0
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
939 </param>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
940
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
941 </xml>
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
942
bb2b0ad44c0e planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
943 </macros>