Mercurial > repos > bgruening > deeptools_bam_coverage

annotate deepTools_macros.xml @ 1:66947f20a9a8 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
author bgruening
date Fri, 18 Dec 2015 08:00:06 -0500
parents af2607db5c89
children fee7b464d8e9
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1 <macros>
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2
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3 <xml name="advancedOpt_scaffold">
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4 <conditional name="advancedOpt">
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5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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6 <option value="no" selected="true">no</option>
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7 <option value="yes">yes</option>
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8 </param>
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9 <when value="no" />
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10 <when value="yes">
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11 <yield/>
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12 </when>
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13 </conditional>
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14 </xml>
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15
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16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
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17 --extendReads $advancedOpt.extendReads
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18 $advancedOpt.ignoreDuplicates
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19 $advancedOpt.centerReads
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20 #if $advancedOpt.minMappingQuality:
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21 --minMappingQuality '$advancedOpt.minMappingQuality'
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22 #end if
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23 #if $advancedOpt.samFlagInclude:
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24 --samFlagInclude $advancedOpt.samFlagInclude
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25 #end if
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26 #if $advancedOpt.samFlagExclude:
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27 --samFlagExclude $advancedOpt.samFlagExclude
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28 #end if
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29 </token>
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30
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31 <xml name="heatmap_options">
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32 <expand macro="zMin_zMax" />
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33 <expand macro="colorMap" />
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34 <expand macro="plotTitle" />
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35 <expand macro="plotNumbers" />
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36 </xml>
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37
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38 <token name="@HEATMAP_OPTIONS@">
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39 #if $zMin:
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40 --zMin $zMin
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41 #end if
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42 #if $zMax:
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43 --zMax $zMax
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44 #end if
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45 --colorMap '$colorMap'
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46 $plotNumbers
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47 </token>
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48
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49 <expand macro="plotTitle" />
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50 <expand macro="plotNumbers" />
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51 <conditional name="output">
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52 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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53 <option value="no" selected="true">no</option>
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54 <option value="yes">yes</option>
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55 </param>
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56 <when value="no" />
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57 <when value="yes">
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58 <expand macro="input_image_file_format"/>
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59 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
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60 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
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61 </when>
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62 </conditional>
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63
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64 <xml name="includeZeros">
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65 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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66 label="Include zeros"
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67 help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
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68 </xml>
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69
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70 <xml name="zMin_zMax">
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71 <param argument="--zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
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72 help="If not specified the value is set automatically."/>
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73 <param argument="--zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
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74 help="If not specified the value is set automatically."/>
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75 </xml>
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76
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77 <xml name="region_limit_operation">
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78 <param argument="--region" type="text" value=""
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79 label="Region of the genome to limit the operation to"
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80 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
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81 </xml>
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82
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83 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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84 <token name="@WRAPPER_VERSION@">2.0.0</token>
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85 <xml name="requirements">
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86 <requirements>
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87 <requirement type="package" version="2.7.10">python</requirement>
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88 <requirement type="binary">@BINARY@</requirement>
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89 <requirement type="package" version="2.0">deepTools</requirement>
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90 <yield />
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91 </requirements>
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92 <expand macro="stdio" />
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93 <version_command>@BINARY@ --version</version_command>
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94 </xml>
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95
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96 <xml name="smoothLength">
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97 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
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98 label="Smooth values using the following length (in bp)"
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99 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
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100 </xml>
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101
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102
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103 <xml name="kmeans_clustering">
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104 <conditional name="used_multiple_regions">
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105 <param name="used_multiple_regions_options" type="select"
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106 label="Did you compute the matrix with more than one groups of regions?"
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107 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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108 <option value="yes">Yes, I used multiple groups of regions</option>
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109 <option value="no">No, I used only one group</option>
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110 </param>
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111 <when value="no">
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112 <conditional name="clustering">
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113 <param name="clustering_options" type="select" label="Clustering algorithm">
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114 <option value="none">No clustering</option>
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115 <option value="kmeans">Kmeans clustering</option>
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116 </param>
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117 <when value="kmeans">
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118 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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119 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
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120 </when>
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121 <when value="none" />
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122 </conditional>
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123 </when>
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124 <when value="yes" />
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125 </conditional>
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126 </xml>
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127
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128 <token name="@KMEANS_CLUSTERING@">
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129 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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130 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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131 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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132 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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133 #end if
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134 #end if
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135 #end if
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136 </token>
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137
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138 <xml name="samFlags">
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139 <param argument="--samFlagInclude" type="integer" optional="True" value=""
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140 label="Include reads based on the SAM flag"
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141 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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142 <param argument="--samFlagExclude" type="integer" optional="True" value=""
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143 label="Exclude reads based on the SAM flag"
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144 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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145 </xml>
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146
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147 <xml name="read_processing_options">
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148 <expand macro="extendReads" />
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149 <expand macro="ignoreDuplicates" />
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150 <expand macro="centerReads" />
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151 <expand macro="minMappingQuality" />
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152 <expand macro="samFlags" />
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153 </xml>
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154
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155 <xml name="plotNumbers">
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156 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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157 label="Plot the correlation value"
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158 help="If set, then the correlation number is plotted on top of the heatmap."/>
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159 </xml>
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160
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161 <xml name="extendReads">
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162 <param argument="--extendReads" type="integer" value="" optional="True"
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163 label="Extend reads to the given average fragment size"
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164 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
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165 By default *each* read mate is extended.
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166 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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167 Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
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168 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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169 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."/>
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170 </xml>
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171
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172 <xml name="corMethod">
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173 <param argument="--corMethod" type="select" label="Correlation method">
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174 <option value="spearman" selected="True">Spearman</option>
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175 <option value="pearson">Pearson</option>
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176 </param>
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177 </xml>
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178
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179 <xml name="distanceBetweenBins">
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180 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
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181 label="Distance between bins"
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182 help="By default, bamCorrelate considers consecutive bins of
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183 the specified 'Bin size'. However, to reduce the
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184 computation time, a larger distance between bins can
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185 by given. Larger distances result in less bins being
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186 considered."/>
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187 </xml>
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188
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189 <xml name="centerReads">
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190 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
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191 label="Center regions with respect to the fragment length"
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192 help="For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. "/>
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193 </xml>
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194
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195 <xml name="ignoreDuplicates">
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196 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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197 label="Ignore duplicates"
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198 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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199 </xml>
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200
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201 <xml name="sortUsing">
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202 <param argument="--sortUsing" type="select" label="Method used for sorting"
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203 help="For each row the method is computed.">
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204 <option value="mean" selected="true">mean</option>
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205 <option value="median">median</option>
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206 <option value="min">min</option>
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207 <option value="max">max</option>
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208 <option value="sum">sum</option>
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209 <option value="region_length">region length</option>
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210 </param>
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211 </xml>
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212
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213 <xml name="sortRegions">
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214 <param argument="--sortRegions" type="select" label="Sort regions"
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215 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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216 <option value="no">no ordering</option>
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217 <option value="descend" selected="true">descending order</option>
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218 <option value="ascend">ascending order</option>
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219 </param>
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220 </xml>
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221
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222 <xml name="minMappingQuality">
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223 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
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224 label="Minimum mapping quality"
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225 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
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226 </xml>
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227
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228 <xml name="skipZeros">
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229 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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230 label ="Skip zeros"
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231 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." />
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232 </xml>
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233
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234 <xml name="fragmentLength">
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235 <param argument="--fragmentLength" type="integer" value="300" min="1"
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236 label="Fragment length used for the sequencing"
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237 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
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238 </xml>
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239
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240 <xml name="scaleFactor">
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241 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
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242 help="When used in combination with --normalizeTo1x or
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243 --normalizeUsingRPKM, the computed scaling factor will
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244 be multiplied by the given scale factor." />
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245 </xml>
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246
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247 <xml name="scaleFactors">
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248 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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249 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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250 </xml>
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251
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252 <xml name="stdio">
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253 <stdio>
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254 <exit_code range="1:" />
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255 <exit_code range=":-1" />
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256 <regex match="Error:" />
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257 <regex match="Exception:" />
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258 <regex match="EXception:" />
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259 <regex match="Traceback" />
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260 </stdio>
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261 </xml>
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262
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263 <xml name="pseudocount">
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264 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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265 </xml>
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266
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267 <token name="@REFERENCES@">
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268
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269 .. class:: infomark
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270
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271 For more information on the tools, please visit our `help site`_.
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272
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273 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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274
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275 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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276
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277 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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278 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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279 .. _help site: https://github.com/fidelram/deepTools/wiki/
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280
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281 </token>
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282 <xml name="citations">
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283 <citations>
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284 <citation type="doi">10.1093/nar/gku365</citation>
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285 <yield />
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286 </citations>
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287 </xml>
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288
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289 <xml name="multiple_input_bams">
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290 <param argument="--bamfiles" type="data" format="bam"
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291 label="Bam file" multiple="true"
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292 help="The BAM file must be sorted."/>
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293 </xml>
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294
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295 <xml name="multiple_input_bigwigs">
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296 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True"
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297 label="Bigwig file"
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298 help="The Bigwig file must be sorted."/>
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299 </xml>
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300
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301 <xml name="plotTitle">
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302 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
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303 label="Title of the plot"
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304 help="Title of the plot, to be printed on top of the generated image." />
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305 </xml>
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306
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307 <token name="@multiple_input_bams@">
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308 <![CDATA[
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309 #set files=[]
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310 #set labels=[]
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311 #for $counter, $bamfile in enumerate($bamfiles):
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312 ln -s "${bamfile}" "./${counter}.bam" &&
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313 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
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314 #silent $files.append('%s.bam' % $counter)
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315 #silent $labels.append('%s' % ($bamfile.display_name))
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316 #end for
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317 ]]>
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318 </token>
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319
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320 <token name="@multiple_input_bigwigs@">
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321 <![CDATA[
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322 #set files=[]
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323 #set labels=[]
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324 #for $counter, $bigwig in enumerate($bigwigfiles):
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325 ln -s "${bigwig}" "${counter}.bw" &&
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326 #silent $files.append('%s.bw' % $counter)
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327 #silent $labels.append('%s' % ($bigwig.display_name))
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328 #end for
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329 ]]>
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330 </token>
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331
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332 <xml name="reference_genome_source">
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333 <conditional name="source">
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334 <param name="ref_source" type="select" label="Reference genome">
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335 <option value="cached">locally cached</option>
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336 <option value="history">in your history</option>
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337 </param>
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338 <when value="cached">
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339 <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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340 <options from_data_table="lastz_seqs">
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341 <filter type="sort_by" column="1" />
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342 <validator type="no_options" message="No indexes are available." />
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343 </options>
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344 </param>
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345 </when>
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346 <when value="history">
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347 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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348 </when>
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349 </conditional>
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350 </xml>
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351
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352 <token name="@reference_genome_source@">
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353 #if $source.ref_source=="history":
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354 --genome $source.input1
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355 #else:
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356 --genome "${source.input1_2bit.fields.path}"
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357 #end if
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358 </token>
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359
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360 <xml name="effectiveGenomeSize">
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361 <conditional name="effectiveGenomeSize">
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362 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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363 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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364 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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365 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
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366 <option value="93260000">ce10 (93260000)</option>
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367 <option value="121400000">dm3 (121400000)</option>
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368 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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369 <option value="2150570000">mm9 (2150570000)</option>
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370 <option value="specific">user specified</option>
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371 </param>
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372 <when value="specific">
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373 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
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374 </when>
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375 <when value="2150570000" />
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376 <when value="2451960000" />
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377 <when value="121400000" />
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378 <when value="93260000" />
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379 </conditional>
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380 </xml>
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381
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382 <xml name="image_file_format">
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383 <param argument="--outFileFormat" type="select" label="Image file format">
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384 <option value="png" selected="true">png</option>
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385 <option value="pdf">pdf</option>
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386 <option value="svg">svg</option>
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387 <option value="eps">eps</option>
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388 </param>
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389 </xml>
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390
1
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391 <xml name="skipNAs">
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392 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
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393 label="Ignore missing data?"
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394 help="This parameter determines if non-covered regions
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395 (regions without overlapping reads) in a bam/bigWig file
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396 should be skipped. The default is to treat those
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397 regions as having a value of zero. The decision to
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398 skip non-covered regions depends on the interpretation
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399 of the data. Non-covered regions may represent for
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400 example repetitive regions that want to be skipped.
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401 (default: False)" />
0
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402 </xml>
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403
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404 <xml name="input_save_matrix_values">
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405 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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406 </xml>
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407
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408 <xml name="input_graphic_output_settings">
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409 <conditional name="output" >
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410 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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411 <option value="no" selected="true">no</option>
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412 <option value="yes">yes</option>
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413 </param>
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414 <when value="no" />
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415 <when value="yes">
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416 <yield />
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417 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
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418 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
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419 </when>
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420 </conditional>
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421 </xml>
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422
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423 <xml name="input_image_file_format">
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424 <param name="outFileFormat" type="select" label="Image file format">
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425 <option value="png" selected="true">png</option>
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426 <option value="pdf">pdf</option>
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427 <option value="svg">svg</option>
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428 <option value="eps">eps</option>
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429 <option value="emf">emf</option>
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430 </param>
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431 </xml>
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432
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433 <xml name="output_image_file_format">
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434 <data format="png" name="outFileName" label="${tool.name} image">
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435 <change_format>
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436 <when input="output.outFileFormat" value="pdf" format="pdf" />
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437 <when input="output.outFileFormat" value="svg" format="svg" />
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438 <when input="output.outFileFormat" value="eps" format="eps" />
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439 <when input="output.outFileFormat" value="emf" format="emf" />
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440 </change_format>
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441 </data>
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442 </xml>
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443
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444 <xml name="output_save_matrix_values">
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445 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
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446 <filter>
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447 ((
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448 output['showOutputSettings'] == 'yes' and
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449 output['saveMatrix'] is True
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450 ))
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451 </filter>
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452 </data>
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453 </xml>
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454
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455 <xml name="output_graphic_outputs">
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456 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
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457 <filter>
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458 ((
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459 output['showOutputSettings'] == 'yes' and
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460 output['saveData'] is True
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461 ))
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462 </filter>
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463 </data>
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464 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
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465 <filter>
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466 ((
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467 output['showOutputSettings'] == 'yes' and
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468 output['saveSortedRegions'] is True
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469 ))
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470 </filter>
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471 </data>
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472 </xml>
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473
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474 <xml name="colorMap">
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475 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
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476 <option value="RdYlBu" selected="true">RdYlBu</option>
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477 <option value="Accent">Accent</option>
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478 <option value="Spectral">Spectral</option>
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479 <option value="Set1">Set1</option>
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480 <option value="Set2">Set2</option>
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481 <option value="Set3">Set3</option>
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482 <option value="Dark2">Dark2</option>
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483 <option value="Reds">Reds</option>
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484 <option value="Oranges">Oranges</option>
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485 <option value="Greens">Greens</option>
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486 <option value="Blues">Blues</option>
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487 <option value="Greys">Greys</option>
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488 <option value="Purples">Purples</option>
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489 <option value="Paired">Paired</option>
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490 <option value="Pastel1">Pastel1</option>
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491 <option value="Pastel2">Pastel2</option>
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492 <option value="spring">spring</option>
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493 <option value="summer">summer</option>
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494 <option value="autumn">autumn</option>
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495 <option value="winter">winter</option>
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496 <option value="hot">hot</option>
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497 <option value="coolwarm">coolwarm</option>
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498 <option value="cool">cool</option>
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499 <option value="seismic">seismic</option>
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500 <option value="terrain">terrain</option>
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501 <option value="ocean">ocean</option>
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502 <option value="rainbow">rainbow</option>
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503 <option value="bone">bone</option>
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504 <option value="flag">flag</option>
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505 <option value="prism">prism</option>
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506 <option value="cubehelix">cubehelix</option>
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507 <option value="binary">binary</option>
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508 <option value="pink">pink</option>
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509 <option value="gray">gray</option>
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510 <option value="copper">copper</option>
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511 <option value="BrBG">BrBG</option>
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512 <option value="BuGn">BuGn</option>
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513 <option value="BuPu">BuPu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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514 <option value="GnBu">GnBu</option>
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515 <option value="OrRd">OrRd</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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516 <option value="PiYG">PiYG</option>
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517 <option value="PRGn">PRGn</option>
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518 <option value="PuOr">PuOr</option>
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519 <option value="PuRd">PuRd</option>
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520 <option value="PuBu">PuBu</option>
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521 <option value="RdBu">RdBu</option>
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522 <option value="RdGy">RdGy</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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523 <option value="RdPu">RdPu</option>
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524 <option value="YlGn">YlGn</option>
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525 <option value="PuBuGn">PuBuGn</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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526 <option value="RdYlGn">RdYlGn</option>
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527 <option value="YlGnBu">YlGnBu</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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528 <option value="YlOrBr">YlOrBr</option>
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529 <option value="YlOrRd">YlOrRd</option>
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530 <option value="gist_gray">gist_gray</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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531 <option value="gist_stern">gist_stern</option>
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532 <option value="gist_earth">gist_earth</option>
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533 <option value="gist_yarg">gist_yarg</option>
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534 <option value="gist_ncar">gist_ncar</option>
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535 <option value="gist_rainbow">gist_rainbow</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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536 <option value="gist_heat">gist_heat</option>
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537 <option value="gnuplot">gnuplot</option>
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538 <option value="gnuplot2">gnuplot2</option>
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539 <option value="CMRmap">CMRmap</option>
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parents:
diff changeset
540 <option value="bwr">bwr</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
541 <option value="hsv">hsv</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
542 <option value="brg">brg</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
543 <option value="jet">jet</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
544 <option value="afmhot">afmhot</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
545 <option value="Accent_r">Accent reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
546 <option value="Spectral_r">Spectral reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
547 <option value="Set1_r">Set1 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
548 <option value="Set2_r">Set2 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
549 <option value="Set3_r">Set3 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
550 <option value="Dark2_r">Dark2 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
551 <option value="Reds_r">Reds reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
552 <option value="Oranges_r">Oranges reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
553 <option value="Greens_r">Greens reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
554 <option value="Blues_r">Blues reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
555 <option value="Greys_r">Greys reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
556 <option value="Purples_r">Purples reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
557 <option value="Paired_r">Paired reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
558 <option value="Pastel1_r">Pastel1 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
559 <option value="Pastel2_r">Pastel2 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
560 <option value="spring_r">spring reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
561 <option value="summer_r">summer reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
562 <option value="autumn_r">autumn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
563 <option value="winter_r">winter reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
564 <option value="hot_r">hot reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
565 <option value="coolwarm_r">coolwarm reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
566 <option value="cool_r">cool reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
567 <option value="seismic_r">seismic reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
568 <option value="terrain_r">terrain reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
569 <option value="ocean_r">ocean reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
570 <option value="rainbow_r">rainbow reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
571 <option value="bone_r">bone reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
572 <option value="flag_r">flag reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
573 <option value="prism_r">prism reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
574 <option value="cubehelix_r">cubehelix reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
575 <option value="binary_r">binary reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
576 <option value="pink_r">pink reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
577 <option value="gray_r">gray reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
578 <option value="copper_r">copper reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
579 <option value="BrBG_r">BrBG reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
580 <option value="BuGn_r">BuGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
581 <option value="BuPu_r">BuPu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
582 <option value="GnBu_r">GnBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
583 <option value="OrRd_r">OrRd reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
584 <option value="PiYG_r">PiYG reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
585 <option value="PRGn_r">PRGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
586 <option value="PuOr_r">PuOr reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
587 <option value="PuRd_r">PuRd reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
588 <option value="PuBu_r">PuBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
589 <option value="RdBu_r">RdBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
590 <option value="RdGy_r">RdGy reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
591 <option value="RdPu_r">RdPu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
592 <option value="YlGn_r">YlGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
593 <option value="PuBuGn_r">PuBuGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
594 <option value="RdYlBu_r">RdYlBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
595 <option value="RdYlGn_r">RdYlGn reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
596 <option value="YlGnBu_r">YlGnBu reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
597 <option value="YlOrBr_r">YlOrBr reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
598 <option value="YlOrRd_r">YlOrRd reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
599 <option value="gist_gray_r">gist_gray reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
600 <option value="gist_stern_r">gist_stern reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
601 <option value="gist_earth_r">gist_earth reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
602 <option value="gist_yarg_r">gist_yarg reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
603 <option value="gist_ncar_r">gist_ncar reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
604 <option value="gist_rainbow_r">gist_rainbow reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
605 <option value="gist_heat_r">gist_heat reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
606 <option value="gnuplot_r">gnuplot reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
607 <option value="gnuplot2_r">gnuplot2 reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
608 <option value="CMRmap_r">CMRmap reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
609 <option value="bwr_r">bwr reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
610 <option value="hsv_r">hsv reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
611 <option value="brg_r">brg reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
612 <option value="jet_r">jet reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
613 <option value="afmhot_r">afmhot reversed</option>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
614 </param>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
615
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
616 </xml>
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
617
af2607db5c89 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
618 </macros>