annotate deepTools_macros.xml @ 5:0bac1f03ef5d draft

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date Tue, 19 Feb 2019 10:06:31 -0500
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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="@WRAPPER_VERSION@">3.2.0.0</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="3.2.0">deeptools</requirement>
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8 <requirement type="package" version="1.9">samtools</requirement>
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9 </requirements>
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10 <expand macro="stdio" />
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11 <version_command>@BINARY@ --version</version_command>
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12 </xml>
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13
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14 <xml name="advancedOpt_scaffold">
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15 <conditional name="advancedOpt">
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16 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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17 <option value="no" selected="true">no</option>
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18 <option value="yes">yes</option>
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19 </param>
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20 <when value="no" />
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21 <when value="yes">
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22 <yield/>
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23 </when>
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24 </conditional>
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25 </xml>
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26
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27 <token name="@PLOTWIDTHHEIGHT@">
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28 --plotWidth '$advancedOpt.plotWidth'
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29 --plotHeight '$advancedOpt.plotHeight'
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30 </token>
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31
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32 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
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33 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
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34 label="Plot height"
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35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
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36
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37 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
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38 label="Plot width"
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39 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
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40 </xml>
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41
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42 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
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43 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
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44 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
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45 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
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46 --extendReads
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47 #end if
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48 $advancedOpt.ignoreDuplicates
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49 $advancedOpt.centerReads
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50 #if $advancedOpt.minMappingQuality:
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51 --minMappingQuality '$advancedOpt.minMappingQuality'
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52 #end if
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53 #if $advancedOpt.samFlagInclude:
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54 --samFlagInclude $advancedOpt.samFlagInclude
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55 #end if
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56 #if $advancedOpt.samFlagExclude:
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57 --samFlagExclude $advancedOpt.samFlagExclude
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58 #end if
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59 #if $advancedOpt.minFragmentLength:
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60 --minFragmentLength $advancedOpt.minFragmentLength
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61 #end if
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62 #if $advancedOpt.maxFragmentLength:
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63 --maxFragmentLength $advancedOpt.maxFragmentLength
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64 #end if
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65 </token>
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66
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67 <token name="@ADVANCED_OPTS_GTF@">
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68 $advancedOpt.metagene
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69 #if $advancedOpt.transcriptID:
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70 --transcriptID $advancedOpt.transcriptID
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71 #end if
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72 #if $advancedOpt.exonID:
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73 --exonID $advancedOpt.exonID
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74 #end if
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75 #if $advancedOpt.transcript_id_designator:
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76 --transcript_id_designator $advancedOpt.transcript_id_designator
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77 #end if
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78 </token>
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79
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80 <xml name="heatmap_options">
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81 <expand macro="zMin_zMax" />
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82 <expand macro="colorMap" />
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83 <expand macro="plotTitle" />
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84 <expand macro="plotNumbers" />
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85 </xml>
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86
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87 <token name="@HEATMAP_OPTIONS@">
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88 #if str($plotting_type.zMin) != "":
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89 --zMin $plotting_type.zMin
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90 #end if
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91 #if str($plotting_type.zMax) != "":
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92 --zMax $plotting_type.zMax
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93 #end if
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94 --colorMap '$plotting_type.colorMap'
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95 $plotting_type.plotNumbers
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96 --plotTitle '$plotting_type.plotTitle'
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97 </token>
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98
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99
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100 <xml name="includeZeros">
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101 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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102 label="Include zeros"
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103 help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />
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104 </xml>
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105
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106 <xml name="zMin_zMax">
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107 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
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108 help="If not specified the value is set automatically."/>
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109 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
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110 help="If not specified the value is set automatically."/>
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111 </xml>
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112
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113 <xml name="region_limit_operation">
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114 <param argument="--region" type="text" value=""
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115 label="Region of the genome to limit the operation to"
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116 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
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117 <sanitizer>
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118 <valid initial="string.letters,string.digits">
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119 <add value="|"/>
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120 <add value=":"/>
2
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121 <add value="."/>
0
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122 </valid>
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123 </sanitizer>
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124 </param>
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125 </xml>
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126
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127 <xml name="smoothLength">
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128 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
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129 label="Smooth values using the following length (in bases)"
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130 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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131 </xml>
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132
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133
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134 <xml name="kmeans_clustering">
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135 <conditional name="used_multiple_regions">
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136 <param name="used_multiple_regions_options" type="select"
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137 label="Did you compute the matrix with more than one groups of regions?"
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138 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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139 <option value="yes">Yes, I used multiple groups of regions</option>
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140 <option value="no">No, I used only one group</option>
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141 </param>
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142 <when value="no">
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143 <conditional name="clustering">
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144 <param name="clustering_options" type="select" label="Clustering algorithm">
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145 <option value="none">No clustering</option>
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146 <option value="kmeans">Kmeans clustering</option>
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147 <option value="hclust">Hierarchical clustering</option>
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148 </param>
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149 <when value="kmeans">
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150 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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151 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
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152 This only works for data that is not grouped, otherwise only the first group will be clustered.
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153 If more specific clustering methods are required it is advisable to save the underlying matrix and
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154 run the clustering using other software."/>
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155 </when>
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156 <when value="hclust">
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157 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
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158 help="WARNING: This option causes the tool to run for a very long time! When this option is
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159 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
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160 This only works for data that is not grouped, otherwise only the first group will be clustered.
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161 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
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162 If more specific clustering methods are required it is advisable to save the underlying matrix and
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163 run the clustering using other software."/>
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164 </when>
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165 <when value="none" />
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166 </conditional>
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167 </when>
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168 <when value="yes" />
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169 </conditional>
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170 </xml>
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171
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172 <token name="@KMEANS_CLUSTERING@">
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173 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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174 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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175 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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176 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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177 #end if
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178 #end if
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179 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
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180 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
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181 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
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182 #end if
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183 #end if
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184 #end if
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185 </token>
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186
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187 <xml name="samFlags">
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188 <param argument="--samFlagInclude" type="integer" optional="True" value=""
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189 label="Include reads based on the SAM flag"
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190 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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191 <param argument="--samFlagExclude" type="integer" optional="True" value=""
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192 label="Exclude reads based on the SAM flag"
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193 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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194 </xml>
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195
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196 <xml name="fragLength">
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197 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
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198 label="Minimum fragment length for inclusion."
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199 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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200 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
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201 label="Maximum fragment length for inclusion."
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202 help="A value of 0 (the default) is equivalent to no maximum." />
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203 </xml>
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204
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205 <xml name="read_processing_options">
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206 <expand macro="extendReads" />
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207 <expand macro="ignoreDuplicates" />
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208 <expand macro="centerReads" />
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209 <expand macro="minMappingQuality" />
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210 <expand macro="samFlags" />
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211 <expand macro="fragLength" />
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212 </xml>
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213
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214 <xml name="gtf_options">
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215 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
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216 label="Use a metagene model"
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217 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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218 <param argument="--transcriptID" optional="True" value="transcript" type="text"
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219 label="transcript designator"
0
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220 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
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221 <param argument="--exonID" optional="True" value="exon" type="text"
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222 label="exon designator"
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223 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
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224 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
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225 label="transcriptID key designator"
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226 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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227 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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228 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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229 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
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230 </xml>
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231
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232
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233 <xml name="plotNumbers">
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234 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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235 label="Plot the correlation value"
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236 help="If set, then the correlation number is plotted on top of the heatmap."/>
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237 </xml>
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238
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239 <xml name="extendReads">
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240 <conditional name="doExtendCustom">
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241 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
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242 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.
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243 By default *each* read mate is extended.
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244 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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245 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
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246 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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247 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
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248 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
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249 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
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250 <option value="custom">A custom length, which will be applied to ALL reads.</option>
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251 </param>
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252 <when value="no" />
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253 <when value="yes" />
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254 <when value="custom">
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255 <param name="extendReadsValue" type="integer" value="300" min="1"
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256 label="Extend reads to the given average fragment size"
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257 help="Extend all reads to this length" />
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258 </when>
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259 </conditional>
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260 </xml>
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261
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262 <xml name="corMethod">
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263 <param argument="--corMethod" type="select" label="Correlation method">
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264 <option value="spearman" selected="True">Spearman</option>
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265 <option value="pearson">Pearson</option>
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266 </param>
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267 </xml>
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268
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269 <xml name="distanceBetweenBins">
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270 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
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271 label="Distance between bins"
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272 help="By default, multiBamSummary considers consecutive bins of
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273 the specified 'Bin size'. However, to reduce the
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274 computation time, a larger distance between bins can
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275 be given. Larger distances result in fewer bins being
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276 considered."/>
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277 </xml>
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278
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279 <xml name="centerReads">
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280 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
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281 label="Center regions with respect to the fragment length"
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282 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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283 </xml>
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284
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285 <xml name="ignoreDuplicates">
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286 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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287 label="Ignore duplicates"
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288 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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289 </xml>
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290
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291 <xml name="sortUsing">
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292 <param argument="--sortUsing" type="select" label="Method used for sorting"
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293 help="For each row the method is computed.">
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294 <option value="mean" selected="true">mean</option>
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295 <option value="median">median</option>
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296 <option value="min">min</option>
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297 <option value="max">max</option>
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298 <option value="sum">sum</option>
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299 <option value="region_length">region length</option>
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300 </param>
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301 </xml>
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302
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303 <xml name="sortRegionsComputeMatrix">
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304 <param argument="--sortRegions" type="select" label="Sort regions"
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305 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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306 <option value="no">no ordering</option>
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307 <option value="keep" selected="true">maintain the same ordering as the input files</option>
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308 <option value="descend">descending order</option>
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309 <option value="ascend">ascending order</option>
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310 </param>
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311 </xml>
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312
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313 <xml name="sortRegions">
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314 <param argument="--sortRegions" type="select" label="Sort regions"
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315 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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316 <option value="no">maintain the same ordering as the input files</option>
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317 <option value="descend" selected="true">descending order</option>
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318 <option value="ascend">ascending order</option>
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319 </param>
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320 </xml>
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321
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322 <xml name="minMappingQuality">
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323 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
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324 label="Minimum mapping quality"
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325 help= "If set, only reads with a mapping quality score at least this high are considered."/>
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326 </xml>
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327
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328 <xml name="skipZeros">
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329 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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330 label ="Skip zeros"
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331 help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />
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332 </xml>
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333
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334 <xml name="fragmentLength">
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335 <param argument="--fragmentLength" type="integer" min="1" optional="true"
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336 label="Fragment length used for the sequencing"
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337 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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338 </xml>
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339
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340 <xml name="scaleFactor">
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341 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
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342 help="The computed scaling factor will be multiplied by this (default 1)." />
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343 </xml>
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344
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345 <xml name="scaleFactors">
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346 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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347 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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348 </xml>
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349
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350 <xml name="stdio">
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351 <stdio>
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352 <exit_code range="1:" />
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353 <exit_code range=":-1" />
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354 <regex match="Error:" />
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355 <regex match="Exception:" />
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356 <regex match="EXception:" />
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357 <regex match="Traceback" />
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358 </stdio>
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359 </xml>
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360
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361 <xml name="pseudocount">
5
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362 <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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363 </xml>
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364
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365 <token name="@REFERENCES@">
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366
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367 .. class:: infomark
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368
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369 For more information on the tools, please visit our `help site`_.
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370
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371 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
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372
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373 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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374
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375 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
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376 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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377 .. _help site: https://deeptools.readthedocs.org/
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378
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379 </token>
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380 <xml name="citations">
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381 <citations>
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382 <citation type="doi">10.1093/nar/gkw257</citation>
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383 <yield />
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384 </citations>
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385 </xml>
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386
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387 <xml name="multiple_input_bams" tokens="MIN">
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388 <conditional name="multibam_conditional">
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389 <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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390 <option value="No" selected="true">No</option>
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391 <option value="Yes">Yes</option>
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392 </param>
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393 <when value="No">
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394 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
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395 label="BAM/CRAM file" multiple="true"
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396 help=""/>
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397 </when>
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398 <when value="Yes">
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399 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
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400 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
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401 </repeat>
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402 </when>
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403 </conditional>
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404 </xml>
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405
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406 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
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407 <conditional name="multibigwig_conditional">
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408 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
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409 is vital to you, select Yes below.">
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410 <option value="No" selected="true">No</option>
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411 <option value="Yes">Yes</option>
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412 </param>
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413 <when value="No">
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414 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
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415 label="@LABEL@"
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416 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
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417 </when>
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418 <when value="Yes">
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419 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
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420 <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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421 </repeat>
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422 </when>
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423 </conditional>
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424 </xml>
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425
5
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426 <xml name="custom_sample_labels">
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427 <conditional name="custom_sample_labels_conditional">
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428 <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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429 <option value="No" selected="true">No, use sample names in the history</option>
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430 <option value="Yes">Yes, I want to specify new labels</option>
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431 </param>
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432 <when value="No">
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433 </when>
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434 <when value="Yes">
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435 <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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436 <sanitizer>
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437 <valid initial="string.printable">
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438 </valid>
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439 </sanitizer>
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440 </param>
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441 </when>
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442 </conditional>
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443 </xml>
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444
0
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445 <xml name="plotTitle">
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446 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
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447 label="Title of the plot"
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448 help="Title of the plot, to be printed on top of the generated image." />
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449 </xml>
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450
5
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451 <xml name="legendLocation">
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452 <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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453 <option value="best" selected="true">Best (automatic)</option>
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454 <option value="upper-right">upper-right</option>
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455 <option value="upper-left">upper-left</option>
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456 <option value="upper-center">upper-center</option>
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457 <option value="lower-right">lower-right</option>
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458 <option value="lower-left">lower-left</option>
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459 <option value="lower-center">lower-center</option>
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460 <option value="center-right">center-right</option>
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461 <option value="center-left">center-left</option>
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462 <option value="center">center</option>
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463 <option value="none">none (only works for heatmaps</option>
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464 </param>
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465 </xml>
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466
0
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467 <xml name="labelRotation">
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468 <param argument="--labelRotation" type="integer" value="0"
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469 label="Rotation of the X-axis labels (in degrees)"
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470 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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471 </xml>
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472
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473
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474 <token name="@multiple_input_bams@">
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475 <![CDATA[
5
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476 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
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477 #set custom_labels=labels
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478 #end if
0
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479 #set files=[]
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480 #set labels=[]
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481 #import re
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482 #if $multibam_conditional.orderMatters == "No":
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483 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
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484 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
2
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485 ln -s '${bamfile}' './${counter}.bam' &&
0
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486 #if $bamfile.ext == 'bam':
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487 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
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488 #else:
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489 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
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490 #end if
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491 #silent $files.append("'%s.bam'" % $counter)
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492 #silent $labels.append("'%s'" % identifier)
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493 #end for
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494 #else:
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495 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
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496 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
2
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497 ln -s '${f.bamfiles}' './${counter}.bam' &&
0
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498 #if $f.bamfiles.ext == 'bam':
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499 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
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500 #else:
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501 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
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502 #end if
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503 #silent $files.append("'%s.bam'" % $counter)
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504 #silent $labels.append("'%s'" % $identifier)
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505 #end for
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506 #end if
5
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507 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
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508 #set labels=custom_labels
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509 #end if
0
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510 ]]>
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511 </token>
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512
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513 <token name="@multiple_input_bigwigs@">
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514 <![CDATA[
5
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515 #if $custom_labels_conditional.custom_labels_select == "Yes":
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516 #set custom_labels=labels
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517 #end if
0
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518 #set files=[]
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519 #set labels=[]
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520 #import re
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521 #if $multibigwig_conditional.orderMatters == "No":
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522 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
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523 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
2
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524 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
0
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525 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
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526 #silent $labels.append("'%s'" % $identifier)
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527 #end for
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528 #else:
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529 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
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530 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
2
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531 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
0
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532 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
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533 #silent $labels.append("'%s'" % $identifier)
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534 #end for
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535 #end if
5
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536 #if $custom_labels_conditional.custom_labels_select == "Yes":
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537 #set labels=custom_labels
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538 #end if
0
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539 ]]>
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540 </token>
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541
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542 <xml name="blacklist">
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543 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
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544 label="Blacklisted regions in BED/GTF format"
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545 help="One or more files containing regions to exclude from the analysis" />
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546 </xml>
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547
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548 <token name="@blacklist@">
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549 <![CDATA[
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550 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
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551 #set blfiles=[]
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552 #for $f in $advancedOpt.blackListFileName:
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553 #silent $blfiles.append("'%s'" % $f)
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554 #end for
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555 #if $blfiles != ["'None'"]:
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556 --blackListFileName #echo ' '.join($blfiles)#
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557 #end if
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558 #end if
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559 ]]>
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560 </token>
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561
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562 <xml name="multiple_bed">
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563 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
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564 label="Regions in BED/GTF format"
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565 help="One or more files containing regions to include in the analysis" />
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566 </xml>
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567
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568 <token name="@multiple_bed@">
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569 <![CDATA[
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570 #set files=[]
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571 #set labels=[]
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572 #for $f in $BED:
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573 #silent $files.append("'%s'" % $f)
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574 #silent $labels.append("'%s'" % $f.display_name)
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575 #end for
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576 #if len($files) > 0:
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577 --BED #echo ' '.join($files)#
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578 --regionLabels #echo ' '.join($labels)#
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579 #end if
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580 ]]>
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581 </token>
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582
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583 <xml name="reference_genome_source">
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584 <conditional name="source">
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585 <param name="ref_source" type="select" label="Reference genome">
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586 <option value="cached">locally cached</option>
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587 <option value="history">in your history</option>
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588 </param>
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589 <when value="cached">
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590 <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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591 <options from_data_table="lastz_seqs">
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592 <filter type="sort_by" column="1" />
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593 <validator type="no_options" message="No indexes are available." />
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594 </options>
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595 </param>
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596 </when>
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597 <when value="history">
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598 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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599 </when>
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600 </conditional>
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601 </xml>
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602
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603 <token name="@reference_genome_source@">
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604 #if $source.ref_source=="history":
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605 --genome $source.input1
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606 #else:
2
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607 --genome '$source.input1_2bit.fields.path'
0
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608 #end if
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609 </token>
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610
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611 <xml name="effectiveGenomeSize">
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612 <conditional name="effectiveGenomeSize">
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613 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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614 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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615 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
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616 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
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617 <option value="93260000">ce10 (93260000)</option>
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618 <option value="130428560">dm3 (130428560)</option>
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619 <option value="125464728">dm6 (125464728)</option>
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620 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
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621 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
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622 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
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623 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
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624 <option value="specific">user specified</option>
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625 </param>
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626 <when value="specific">
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627 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
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628 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
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629 </when>
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630 <when value="93260000" />
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631 <when value="130428560" />
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632 <when value="125464728" />
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633 <when value="2685511504" />
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634 <when value="2701495761" />
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635 <when value="2304947926" />
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636 <when value="2308125349" />
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637 </conditional>
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638 </xml>
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639
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640 <xml name="skipNAs">
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641 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
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642 label="Ignore missing data?"
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643 help="This parameter determines if non-covered regions
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644 (regions without overlapping reads) in a bam/bigWig file
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645 should be skipped. The default is to treat those
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646 regions as having a value of zero. The decision to
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647 skip non-covered regions depends on the interpretation
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648 of the data. Non-covered regions may represent, for
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649 example, repetitive regions that should be ignored.
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650 (default: False)" />
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651 </xml>
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652
3
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653 <xml name="exactScaling">
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654 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
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655 label="Compute an exact scaling factor"
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656 help="Compute an exact scaling factor rather than one based on
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657 sampled reads. This is only useful in cases where you are
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658 filtering some alignments out AND this are both rare and
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659 tend to clump together in the genome. In such cases the
11f1d6fcf2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb
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660 region-based sampling employed by deepTools would produce
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661 inaccurate scaling factors. Note that this option results
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662 in the process taking significantly more time to complete." />
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663 </xml>
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664
0
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665 <xml name="input_save_matrix_values">
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666 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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667 </xml>
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668
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669 <xml name="input_graphic_output_settings">
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670 <conditional name="output" >
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671 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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672 <option value="no" selected="true">no</option>
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673 <option value="yes">yes</option>
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674 </param>
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675 <when value="no" />
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676 <when value="yes">
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677 <yield />
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678 <param name="saveSortedRegions" type="boolean"
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679 argument="--outFileSortedRegions"
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680 label="Save the regions after skipping zeros or min/max threshold values"
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681 help="The order of the regions in the file follows the sorting order selected. This is useful,
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682 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
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683 </when>
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684 </conditional>
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685 </xml>
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686
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687
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688 <xml name="input_image_file_format">
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689 <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.">
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690 <option value="png" selected="true">png</option>
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691 <option value="pdf">pdf</option>
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692 <option value="svg">svg</option>
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693 <option value="eps">eps</option>
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694 <option value="plotly">plotly</option>
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695 </param>
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696 </xml>
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697
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698 <xml name="output_dpi">
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diff changeset
699 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
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700 label="Image dpi" help=""/>
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701 </xml>
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702
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703 <xml name="output_image_file_format">
4
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704 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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705 <change_format>
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706 <when input="output.outFileFormat" value="pdf" format="pdf" />
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707 <when input="output.outFileFormat" value="svg" format="svg" />
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708 <when input="output.outFileFormat" value="eps" format="eps" />
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709 <when input="output.outFileFormat" value="plotly" format="html" />
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710 </change_format>
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711 </data>
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712 </xml>
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713
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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714 <xml name="output_image_file_format_not_nested">
4
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diff changeset
715 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
0
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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716 <change_format>
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717 <when input="outFileFormat" value="pdf" format="pdf" />
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718 <when input="outFileFormat" value="svg" format="svg" />
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719 <when input="outFileFormat" value="eps" format="eps" />
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720 <when input="outFileFormat" value="plotly" format="html" />
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721 </change_format>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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722 </data>
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723 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
724
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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725 <xml name="output_save_matrix_values">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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726 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
727 <filter>
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diff changeset
728 ((
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
729 output['showOutputSettings'] == 'yes' and
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
730 output['saveMatrix'] is True
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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731 ))
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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732 </filter>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
733 </data>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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734 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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735
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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736 <xml name="output_graphic_outputs">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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737 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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738 <filter>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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739 ((
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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740 output['showOutputSettings'] == 'yes' and
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
741 output['saveSortedRegions'] is True
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742 ))
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743 </filter>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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744 </data>
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745 </xml>
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746
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
747 <xml name="colorMap">
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
748 <param name="colorMap" type="select" label="Color map to use for the heatmap"
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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749 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
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750 <option value="RdYlBu" selected="true">RdYlBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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751 <option value="Accent">Accent</option>
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752 <option value="Spectral">Spectral</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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753 <option value="Set1">Set1</option>
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754 <option value="Set2">Set2</option>
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755 <option value="Set3">Set3</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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756 <option value="Dark2">Dark2</option>
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757 <option value="Reds">Reds</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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758 <option value="Oranges">Oranges</option>
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759 <option value="Greens">Greens</option>
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760 <option value="Blues">Blues</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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761 <option value="Greys">Greys</option>
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762 <option value="Purples">Purples</option>
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763 <option value="Paired">Paired</option>
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764 <option value="Pastel1">Pastel1</option>
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765 <option value="Pastel2">Pastel2</option>
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766 <option value="spring">spring</option>
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767 <option value="summer">summer</option>
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768 <option value="autumn">autumn</option>
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769 <option value="winter">winter</option>
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770 <option value="hot">hot</option>
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771 <option value="coolwarm">coolwarm</option>
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772 <option value="cool">cool</option>
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773 <option value="seismic">seismic</option>
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774 <option value="terrain">terrain</option>
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775 <option value="ocean">ocean</option>
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parents:
diff changeset
776 <option value="rainbow">rainbow</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
777 <option value="bone">bone</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
778 <option value="flag">flag</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
779 <option value="prism">prism</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
780 <option value="cubehelix">cubehelix</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
781 <option value="binary">binary</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
782 <option value="pink">pink</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
783 <option value="gray">gray</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
784 <option value="copper">copper</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
785 <option value="BrBG">BrBG</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
786 <option value="BuGn">BuGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
787 <option value="BuPu">BuPu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
788 <option value="GnBu">GnBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
789 <option value="OrRd">OrRd</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
790 <option value="PiYG">PiYG</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
791 <option value="PRGn">PRGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
792 <option value="PuOr">PuOr</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
793 <option value="PuRd">PuRd</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
794 <option value="PuBu">PuBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
795 <option value="RdBu">RdBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
796 <option value="RdGy">RdGy</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
797 <option value="RdPu">RdPu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
798 <option value="YlGn">YlGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
799 <option value="PuBuGn">PuBuGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
800 <option value="RdYlGn">RdYlGn</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
801 <option value="YlGnBu">YlGnBu</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
802 <option value="YlOrBr">YlOrBr</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
803 <option value="YlOrRd">YlOrRd</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
804 <option value="gist_gray">gist_gray</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
805 <option value="gist_stern">gist_stern</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
806 <option value="gist_earth">gist_earth</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
807 <option value="gist_yarg">gist_yarg</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
808 <option value="gist_ncar">gist_ncar</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
809 <option value="gist_rainbow">gist_rainbow</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
810 <option value="gist_heat">gist_heat</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
811 <option value="gnuplot">gnuplot</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
812 <option value="gnuplot2">gnuplot2</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
813 <option value="CMRmap">CMRmap</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
814 <option value="bwr">bwr</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
815 <option value="hsv">hsv</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
816 <option value="brg">brg</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
817 <option value="jet">jet</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
818 <option value="afmhot">afmhot</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
819 <option value="Accent_r">Accent reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
820 <option value="Spectral_r">Spectral reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
821 <option value="Set1_r">Set1 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
822 <option value="Set2_r">Set2 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
823 <option value="Set3_r">Set3 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
824 <option value="Dark2_r">Dark2 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
825 <option value="Reds_r">Reds reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
826 <option value="Oranges_r">Oranges reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
827 <option value="Greens_r">Greens reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
828 <option value="Blues_r">Blues reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
829 <option value="Greys_r">Greys reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
830 <option value="Purples_r">Purples reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
831 <option value="Paired_r">Paired reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
832 <option value="Pastel1_r">Pastel1 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
833 <option value="Pastel2_r">Pastel2 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
834 <option value="spring_r">spring reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
835 <option value="summer_r">summer reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
836 <option value="autumn_r">autumn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
837 <option value="winter_r">winter reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
838 <option value="hot_r">hot reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
839 <option value="coolwarm_r">coolwarm reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
840 <option value="cool_r">cool reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
841 <option value="seismic_r">seismic reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
842 <option value="terrain_r">terrain reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
843 <option value="ocean_r">ocean reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
844 <option value="rainbow_r">rainbow reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
845 <option value="bone_r">bone reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
846 <option value="flag_r">flag reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
847 <option value="prism_r">prism reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
848 <option value="cubehelix_r">cubehelix reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
849 <option value="binary_r">binary reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
850 <option value="pink_r">pink reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
851 <option value="gray_r">gray reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
852 <option value="copper_r">copper reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
853 <option value="BrBG_r">BrBG reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
854 <option value="BuGn_r">BuGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
855 <option value="BuPu_r">BuPu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
856 <option value="GnBu_r">GnBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
857 <option value="OrRd_r">OrRd reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
858 <option value="PiYG_r">PiYG reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
859 <option value="PRGn_r">PRGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
860 <option value="PuOr_r">PuOr reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
861 <option value="PuRd_r">PuRd reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
862 <option value="PuBu_r">PuBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
863 <option value="RdBu_r">RdBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
864 <option value="RdGy_r">RdGy reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
865 <option value="RdPu_r">RdPu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
866 <option value="YlGn_r">YlGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
867 <option value="PuBuGn_r">PuBuGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
868 <option value="RdYlBu_r">RdYlBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
869 <option value="RdYlGn_r">RdYlGn reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
870 <option value="YlGnBu_r">YlGnBu reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
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871 <option value="YlOrBr_r">YlOrBr reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
872 <option value="YlOrRd_r">YlOrRd reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
873 <option value="gist_gray_r">gist_gray reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
874 <option value="gist_stern_r">gist_stern reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff changeset
875 <option value="gist_earth_r">gist_earth reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
876 <option value="gist_yarg_r">gist_yarg reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
877 <option value="gist_ncar_r">gist_ncar reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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diff changeset
878 <option value="gist_rainbow_r">gist_rainbow reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
879 <option value="gist_heat_r">gist_heat reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
880 <option value="gnuplot_r">gnuplot reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
881 <option value="gnuplot2_r">gnuplot2 reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
882 <option value="CMRmap_r">CMRmap reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
883 <option value="bwr_r">bwr reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
884 <option value="hsv_r">hsv reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
885 <option value="brg_r">brg reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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parents:
diff changeset
886 <option value="jet_r">jet reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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887 <option value="afmhot_r">afmhot reversed</option>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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888 </param>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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889
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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890 </xml>
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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891
dfc5a344e2c2 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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892 </macros>