Mercurial > repos > bgruening > deeptools_plot_coverage
annotate deepTools_macros.xml @ 0:fd4a79e7e5f0 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
author | bgruening |
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date | Mon, 21 Dec 2015 19:06:15 -0500 |
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children | 9f2b016177e7 |
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fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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1 <macros> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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2 |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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3 <xml name="advancedOpt_scaffold"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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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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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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8 </param> |
fd4a79e7e5f0
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9 <when value="no" /> |
fd4a79e7e5f0
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10 <when value="yes"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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11 <yield/> |
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12 </when> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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13 </conditional> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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14 </xml> |
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15 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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16 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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17 #if $advancedOpt.doExtendCustom.doExtend == 'custom': |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes': |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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20 --extendReads |
fd4a79e7e5f0
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21 #end if |
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22 $advancedOpt.ignoreDuplicates |
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23 $advancedOpt.centerReads |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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24 #if $advancedOpt.minMappingQuality: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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25 --minMappingQuality '$advancedOpt.minMappingQuality' |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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26 #end if |
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27 #if $advancedOpt.samFlagInclude: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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28 --samFlagInclude $advancedOpt.samFlagInclude |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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29 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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30 #if $advancedOpt.samFlagExclude: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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31 --samFlagExclude $advancedOpt.samFlagExclude |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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32 #end if |
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33 </token> |
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34 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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35 <xml name="heatmap_options"> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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36 <expand macro="zMin_zMax" /> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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37 <expand macro="colorMap" /> |
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38 <expand macro="plotTitle" /> |
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39 <expand macro="plotNumbers" /> |
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40 </xml> |
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41 |
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42 <token name="@HEATMAP_OPTIONS@"> |
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43 #if $plotting_type.zMin: |
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44 --zMin $plotting_type.zMin |
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45 #end if |
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46 #if $plotting_type.zMax: |
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47 --zMax $plotting_type.zMax |
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48 #end if |
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49 --colorMap '$plotting_type.colorMap' |
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50 $plotting_type.plotNumbers |
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51 --plotTitle '$plotting_type.plotTitle' |
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52 </token> |
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53 |
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54 |
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55 <xml name="includeZeros"> |
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56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
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57 label="Include zeros" |
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58 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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59 </xml> |
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60 |
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61 <xml name="zMin_zMax"> |
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62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities" |
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63 help="If not specified the value is set automatically."/> |
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64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities" |
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65 help="If not specified the value is set automatically."/> |
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66 </xml> |
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67 |
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68 <xml name="region_limit_operation"> |
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69 <param argument="--region" type="text" value="" |
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70 label="Region of the genome to limit the operation to" |
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71 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> |
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72 </xml> |
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73 |
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74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
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75 <token name="@WRAPPER_VERSION@">2.0.0</token> |
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76 <xml name="requirements"> |
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77 <requirements> |
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78 <requirement type="package" version="2.7.10">python</requirement> |
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79 <requirement type="binary">@BINARY@</requirement> |
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80 <requirement type="package" version="2.0">deepTools</requirement> |
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81 <yield /> |
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82 </requirements> |
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83 <expand macro="stdio" /> |
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84 <version_command>@BINARY@ --version</version_command> |
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85 </xml> |
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86 |
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87 <xml name="smoothLength"> |
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88 <param argument="--smoothLength" type="integer" value="" optional="True" min="1" |
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89 label="Smooth values using the following length (in bp)" |
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90 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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91 </xml> |
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92 |
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93 |
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94 <xml name="kmeans_clustering"> |
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95 <conditional name="used_multiple_regions"> |
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96 <param name="used_multiple_regions_options" type="select" |
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97 label="Did you compute the matrix with more than one groups of regions?" |
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98 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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99 <option value="yes">Yes, I used multiple groups of regions</option> |
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100 <option value="no">No, I used only one group</option> |
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101 </param> |
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102 <when value="no"> |
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103 <conditional name="clustering"> |
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104 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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105 <option value="none">No clustering</option> |
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106 <option value="kmeans">Kmeans clustering</option> |
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107 </param> |
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108 <when value="kmeans"> |
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109 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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110 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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111 </when> |
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112 <when value="none" /> |
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113 </conditional> |
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114 </when> |
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115 <when value="yes" /> |
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116 </conditional> |
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117 </xml> |
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118 |
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119 <token name="@KMEANS_CLUSTERING@"> |
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120 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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121 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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122 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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123 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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124 #end if |
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125 #end if |
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126 #end if |
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127 </token> |
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128 |
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129 <xml name="samFlags"> |
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130 <param argument="--samFlagInclude" type="integer" optional="True" value="" |
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131 label="Include reads based on the SAM flag" |
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132 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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133 <param argument="--samFlagExclude" type="integer" optional="True" value="" |
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134 label="Exclude reads based on the SAM flag" |
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135 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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136 </xml> |
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137 |
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138 <xml name="read_processing_options"> |
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139 <expand macro="extendReads" /> |
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140 <expand macro="ignoreDuplicates" /> |
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141 <expand macro="centerReads" /> |
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142 <expand macro="minMappingQuality" /> |
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143 <expand macro="samFlags" /> |
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144 </xml> |
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145 |
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146 <xml name="plotNumbers"> |
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147 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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148 label="Plot the correlation value" |
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149 help="If set, then the correlation number is plotted on top of the heatmap."/> |
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150 </xml> |
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151 |
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152 <xml name="extendReads"> |
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153 <conditional name="doExtendCustom"> |
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154 <param name="doExtend" type="select" label="Extend reads to the given average fragment size." |
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155 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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156 By default *each* read mate is extended. |
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157 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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158 Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value. |
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159 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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160 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> |
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161 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> |
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162 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> |
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163 <option value="custom">A custom length, which will be applied to ALL reads.</option> |
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164 </param> |
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165 <when value="no" /> |
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166 <when value="yes" /> |
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167 <when value="custom"> |
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168 <param name="extendReadsValue" type="integer" value="300" min="1" |
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169 label="Extend reads to the given average fragment size" |
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170 help="Extend all reads to this length" /> |
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171 </when> |
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172 </conditional> |
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173 </xml> |
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174 |
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175 <xml name="corMethod"> |
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176 <param argument="--corMethod" type="select" label="Correlation method"> |
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177 <option value="spearman" selected="True">Spearman</option> |
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178 <option value="pearson">Pearson</option> |
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179 </param> |
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180 </xml> |
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181 |
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182 <xml name="distanceBetweenBins"> |
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183 <param argument="--distanceBetweenBins" type="integer" value="0" min="0" |
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184 label="Distance between bins" |
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185 help="By default, bamCorrelate considers consecutive bins of |
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186 the specified 'Bin size'. However, to reduce the |
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187 computation time, a larger distance between bins can |
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188 by given. Larger distances result in less bins being |
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189 considered."/> |
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190 </xml> |
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191 |
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192 <xml name="centerReads"> |
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193 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" |
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194 label="Center regions with respect to the fragment length" |
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195 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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196 </xml> |
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197 |
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198 <xml name="ignoreDuplicates"> |
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199 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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200 label="Ignore duplicates" |
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201 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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202 </xml> |
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203 |
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204 <xml name="sortUsing"> |
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205 <param argument="--sortUsing" type="select" label="Method used for sorting" |
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206 help="For each row the method is computed."> |
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207 <option value="mean" selected="true">mean</option> |
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208 <option value="median">median</option> |
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209 <option value="min">min</option> |
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210 <option value="max">max</option> |
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211 <option value="sum">sum</option> |
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212 <option value="region_length">region length</option> |
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213 </param> |
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214 </xml> |
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215 |
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216 <xml name="sortRegions"> |
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217 <param argument="--sortRegions" type="select" label="Sort regions" |
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218 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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219 <option value="no">no ordering</option> |
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220 <option value="descend" selected="true">descending order</option> |
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221 <option value="ascend">ascending order</option> |
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222 </param> |
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223 </xml> |
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224 |
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225 <xml name="minMappingQuality"> |
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226 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1" |
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227 label="Minimum mapping quality" |
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228 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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229 </xml> |
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230 |
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231 <xml name="skipZeros"> |
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232 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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233 label ="Skip zeros" |
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234 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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235 </xml> |
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236 |
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237 <xml name="fragmentLength"> |
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238 <param argument="--fragmentLength" type="integer" value="300" min="1" |
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239 label="Fragment length used for the sequencing" |
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240 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/> |
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241 </xml> |
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242 |
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243 <xml name="scaleFactor"> |
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244 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" |
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245 help="When used in combination with --normalizeTo1x or |
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246 --normalizeUsingRPKM, the computed scaling factor will |
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247 be multiplied by the given scale factor." /> |
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248 </xml> |
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249 |
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250 <xml name="scaleFactors"> |
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251 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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252 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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253 </xml> |
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254 |
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255 <xml name="stdio"> |
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256 <stdio> |
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257 <exit_code range="1:" /> |
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258 <exit_code range=":-1" /> |
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259 <regex match="Error:" /> |
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260 <regex match="Exception:" /> |
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261 <regex match="EXception:" /> |
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262 <regex match="Traceback" /> |
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263 </stdio> |
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264 </xml> |
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265 |
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266 <xml name="pseudocount"> |
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267 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
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268 </xml> |
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269 |
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270 <token name="@REFERENCES@"> |
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271 |
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272 .. class:: infomark |
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273 |
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274 For more information on the tools, please visit our `help site`_. |
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275 |
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276 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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277 |
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278 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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279 |
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280 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac |
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281 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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282 .. _help site: https://deeptools.readthedocs.org/ |
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283 |
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284 </token> |
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285 <xml name="citations"> |
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286 <citations> |
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287 <citation type="doi">10.1093/nar/gku365</citation> |
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288 <yield /> |
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289 </citations> |
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290 </xml> |
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291 |
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292 <xml name="multiple_input_bams"> |
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293 <param argument="--bamfiles" type="data" format="bam" min="2" |
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294 label="Bam file" multiple="true" |
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295 help="The BAM file must be sorted."/> |
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296 </xml> |
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297 |
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298 <xml name="multiple_input_bigwigs"> |
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299 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" |
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300 label="Bigwig file" |
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301 help="The Bigwig file must be sorted."/> |
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302 </xml> |
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303 |
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304 <xml name="plotTitle"> |
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305 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
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306 label="Title of the plot" |
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307 help="Title of the plot, to be printed on top of the generated image." /> |
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308 </xml> |
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309 |
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310 <token name="@multiple_input_bams@"> |
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311 <![CDATA[ |
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312 #set files=[] |
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313 #set labels=[] |
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314 #for $counter, $bamfile in enumerate($bamfiles): |
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315 ln -s "${bamfile}" "./${counter}.bam" && |
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316 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && |
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317 #silent $files.append('%s.bam' % $counter) |
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318 #silent $labels.append('%s' % ($bamfile.display_name)) |
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319 #end for |
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320 ]]> |
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321 </token> |
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322 |
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323 <token name="@multiple_input_bigwigs@"> |
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324 <![CDATA[ |
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325 #set files=[] |
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326 #set labels=[] |
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327 #for $counter, $bigwig in enumerate($bigwigfiles): |
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328 ln -s "${bigwig}" "${counter}.bw" && |
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329 #silent $files.append('%s.bw' % $counter) |
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330 #silent $labels.append('%s' % ($bigwig.display_name)) |
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331 #end for |
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332 ]]> |
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333 </token> |
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334 |
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335 <xml name="reference_genome_source"> |
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336 <conditional name="source"> |
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337 <param name="ref_source" type="select" label="Reference genome"> |
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338 <option value="cached">locally cached</option> |
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339 <option value="history">in your history</option> |
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340 </param> |
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341 <when value="cached"> |
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342 <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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343 <options from_data_table="lastz_seqs"> |
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344 <filter type="sort_by" column="1" /> |
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345 <validator type="no_options" message="No indexes are available." /> |
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346 </options> |
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347 </param> |
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348 </when> |
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349 <when value="history"> |
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350 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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351 </when> |
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352 </conditional> |
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353 </xml> |
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354 |
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355 <token name="@reference_genome_source@"> |
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356 #if $source.ref_source=="history": |
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357 --genome $source.input1 |
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358 #else: |
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359 --genome "$source.input1_2bit.fields.path" |
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360 #end if |
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361 </token> |
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362 |
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363 <xml name="effectiveGenomeSize"> |
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364 <conditional name="effectiveGenomeSize"> |
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365 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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366 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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367 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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368 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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369 <option value="93260000">ce10 (93260000)</option> |
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370 <option value="121400000">dm3 (121400000)</option> |
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371 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
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372 <option value="2150570000">mm9 (2150570000)</option> |
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373 <option value="specific">user specified</option> |
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374 </param> |
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375 <when value="specific"> |
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376 <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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377 </when> |
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378 <when value="2150570000" /> |
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379 <when value="2451960000" /> |
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380 <when value="121400000" /> |
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381 <when value="93260000" /> |
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382 </conditional> |
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383 </xml> |
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384 |
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385 <xml name="skipNAs"> |
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386 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" |
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387 label="Ignore missing data?" |
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388 help="This parameter determines if non-covered regions |
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389 (regions without overlapping reads) in a bam/bigWig file |
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390 should be skipped. The default is to treat those |
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391 regions as having a value of zero. The decision to |
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392 skip non-covered regions depends on the interpretation |
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393 of the data. Non-covered regions may represent for |
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394 example repetitive regions that want to be skipped. |
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395 (default: False)" /> |
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396 </xml> |
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397 |
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398 <xml name="input_save_matrix_values"> |
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399 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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400 </xml> |
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401 |
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402 <xml name="input_graphic_output_settings"> |
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403 <conditional name="output" > |
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404 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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405 <option value="no" selected="true">no</option> |
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406 <option value="yes">yes</option> |
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407 </param> |
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408 <when value="no" /> |
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409 <when value="yes"> |
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410 <yield /> |
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411 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> |
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412 <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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413 </when> |
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414 </conditional> |
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415 </xml> |
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416 |
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417 |
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418 <xml name="input_image_file_format"> |
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419 <param argument="--outFileFormat" type="select" label="Image file format"> |
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420 <option value="png" selected="true">png</option> |
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421 <option value="pdf">pdf</option> |
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422 <option value="svg">svg</option> |
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423 <option value="eps">eps</option> |
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424 </param> |
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425 </xml> |
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426 |
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427 <xml name="output_image_file_format"> |
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428 <data format="png" name="outFileName" label="${tool.name} image"> |
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429 <change_format> |
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430 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
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431 <when input="output.outFileFormat" value="svg" format="svg" /> |
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432 <when input="output.outFileFormat" value="eps" format="eps" /> |
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433 </change_format> |
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434 </data> |
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435 </xml> |
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436 |
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437 <xml name="output_image_file_format_not_nested"> |
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438 <data format="png" name="outFileName" label="${tool.name} image"> |
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439 <change_format> |
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440 <when input="outFileFormat" value="pdf" format="pdf" /> |
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441 <when input="outFileFormat" value="svg" format="svg" /> |
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442 <when input="outFileFormat" value="eps" format="eps" /> |
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443 </change_format> |
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444 </data> |
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445 </xml> |
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446 |
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447 <xml name="output_save_matrix_values"> |
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448 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
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449 <filter> |
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450 (( |
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451 output['showOutputSettings'] == 'yes' and |
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452 output['saveMatrix'] is True |
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453 )) |
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454 </filter> |
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455 </data> |
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456 </xml> |
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457 |
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458 <xml name="output_graphic_outputs"> |
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459 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
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460 <filter> |
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461 (( |
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462 output['showOutputSettings'] == 'yes' and |
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463 output['saveData'] is True |
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464 )) |
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465 </filter> |
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466 </data> |
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467 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
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468 <filter> |
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469 (( |
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470 output['showOutputSettings'] == 'yes' and |
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471 output['saveSortedRegions'] is True |
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472 )) |
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473 </filter> |
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474 </data> |
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475 </xml> |
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476 |
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477 <xml name="colorMap"> |
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478 <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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479 <option value="RdYlBu" selected="true">RdYlBu</option> |
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480 <option value="Accent">Accent</option> |
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481 <option value="Spectral">Spectral</option> |
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482 <option value="Set1">Set1</option> |
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483 <option value="Set2">Set2</option> |
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484 <option value="Set3">Set3</option> |
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485 <option value="Dark2">Dark2</option> |
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486 <option value="Reds">Reds</option> |
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487 <option value="Oranges">Oranges</option> |
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488 <option value="Greens">Greens</option> |
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489 <option value="Blues">Blues</option> |
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490 <option value="Greys">Greys</option> |
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491 <option value="Purples">Purples</option> |
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492 <option value="Paired">Paired</option> |
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493 <option value="Pastel1">Pastel1</option> |
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494 <option value="Pastel2">Pastel2</option> |
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495 <option value="spring">spring</option> |
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496 <option value="summer">summer</option> |
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497 <option value="autumn">autumn</option> |
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498 <option value="winter">winter</option> |
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499 <option value="hot">hot</option> |
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500 <option value="coolwarm">coolwarm</option> |
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501 <option value="cool">cool</option> |
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502 <option value="seismic">seismic</option> |
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503 <option value="terrain">terrain</option> |
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504 <option value="ocean">ocean</option> |
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505 <option value="rainbow">rainbow</option> |
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506 <option value="bone">bone</option> |
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507 <option value="flag">flag</option> |
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508 <option value="prism">prism</option> |
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509 <option value="cubehelix">cubehelix</option> |
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510 <option value="binary">binary</option> |
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511 <option value="pink">pink</option> |
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512 <option value="gray">gray</option> |
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513 <option value="copper">copper</option> |
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514 <option value="BrBG">BrBG</option> |
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515 <option value="BuGn">BuGn</option> |
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516 <option value="BuPu">BuPu</option> |
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517 <option value="GnBu">GnBu</option> |
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518 <option value="OrRd">OrRd</option> |
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519 <option value="PiYG">PiYG</option> |
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520 <option value="PRGn">PRGn</option> |
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521 <option value="PuOr">PuOr</option> |
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522 <option value="PuRd">PuRd</option> |
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523 <option value="PuBu">PuBu</option> |
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524 <option value="RdBu">RdBu</option> |
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525 <option value="RdGy">RdGy</option> |
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526 <option value="RdPu">RdPu</option> |
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527 <option value="YlGn">YlGn</option> |
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528 <option value="PuBuGn">PuBuGn</option> |
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529 <option value="RdYlGn">RdYlGn</option> |
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530 <option value="YlGnBu">YlGnBu</option> |
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531 <option value="YlOrBr">YlOrBr</option> |
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532 <option value="YlOrRd">YlOrRd</option> |
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533 <option value="gist_gray">gist_gray</option> |
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534 <option value="gist_stern">gist_stern</option> |
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535 <option value="gist_earth">gist_earth</option> |
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536 <option value="gist_yarg">gist_yarg</option> |
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537 <option value="gist_ncar">gist_ncar</option> |
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538 <option value="gist_rainbow">gist_rainbow</option> |
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539 <option value="gist_heat">gist_heat</option> |
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540 <option value="gnuplot">gnuplot</option> |
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541 <option value="gnuplot2">gnuplot2</option> |
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542 <option value="CMRmap">CMRmap</option> |
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543 <option value="bwr">bwr</option> |
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544 <option value="hsv">hsv</option> |
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545 <option value="brg">brg</option> |
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546 <option value="jet">jet</option> |
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547 <option value="afmhot">afmhot</option> |
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548 <option value="Accent_r">Accent reversed</option> |
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549 <option value="Spectral_r">Spectral reversed</option> |
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550 <option value="Set1_r">Set1 reversed</option> |
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551 <option value="Set2_r">Set2 reversed</option> |
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552 <option value="Set3_r">Set3 reversed</option> |
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553 <option value="Dark2_r">Dark2 reversed</option> |
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554 <option value="Reds_r">Reds reversed</option> |
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555 <option value="Oranges_r">Oranges reversed</option> |
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556 <option value="Greens_r">Greens reversed</option> |
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557 <option value="Blues_r">Blues reversed</option> |
fd4a79e7e5f0
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|
558 <option value="Greys_r">Greys reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
bgruening
parents:
diff
changeset
|
559 <option value="Purples_r">Purples reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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parents:
diff
changeset
|
560 <option value="Paired_r">Paired reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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diff
changeset
|
561 <option value="Pastel1_r">Pastel1 reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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|
562 <option value="Pastel2_r">Pastel2 reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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diff
changeset
|
563 <option value="spring_r">spring reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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parents:
diff
changeset
|
564 <option value="summer_r">summer reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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parents:
diff
changeset
|
565 <option value="autumn_r">autumn reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
bgruening
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diff
changeset
|
566 <option value="winter_r">winter reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
bgruening
parents:
diff
changeset
|
567 <option value="hot_r">hot reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
bgruening
parents:
diff
changeset
|
568 <option value="coolwarm_r">coolwarm reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
bgruening
parents:
diff
changeset
|
569 <option value="cool_r">cool reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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parents:
diff
changeset
|
570 <option value="seismic_r">seismic reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
571 <option value="terrain_r">terrain reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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parents:
diff
changeset
|
572 <option value="ocean_r">ocean reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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parents:
diff
changeset
|
573 <option value="rainbow_r">rainbow reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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parents:
diff
changeset
|
574 <option value="bone_r">bone reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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diff
changeset
|
575 <option value="flag_r">flag reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
576 <option value="prism_r">prism reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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diff
changeset
|
577 <option value="cubehelix_r">cubehelix reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
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578 <option value="binary_r">binary reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
579 <option value="pink_r">pink reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
580 <option value="gray_r">gray reversed</option> |
fd4a79e7e5f0
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changeset
|
581 <option value="copper_r">copper reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
582 <option value="BrBG_r">BrBG reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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|
583 <option value="BuGn_r">BuGn reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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diff
changeset
|
584 <option value="BuPu_r">BuPu reversed</option> |
fd4a79e7e5f0
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changeset
|
585 <option value="GnBu_r">GnBu reversed</option> |
fd4a79e7e5f0
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changeset
|
586 <option value="OrRd_r">OrRd reversed</option> |
fd4a79e7e5f0
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|
587 <option value="PiYG_r">PiYG reversed</option> |
fd4a79e7e5f0
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|
588 <option value="PRGn_r">PRGn reversed</option> |
fd4a79e7e5f0
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changeset
|
589 <option value="PuOr_r">PuOr reversed</option> |
fd4a79e7e5f0
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changeset
|
590 <option value="PuRd_r">PuRd reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
591 <option value="PuBu_r">PuBu reversed</option> |
fd4a79e7e5f0
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changeset
|
592 <option value="RdBu_r">RdBu reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
593 <option value="RdGy_r">RdGy reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
594 <option value="RdPu_r">RdPu reversed</option> |
fd4a79e7e5f0
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changeset
|
595 <option value="YlGn_r">YlGn reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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|
596 <option value="PuBuGn_r">PuBuGn reversed</option> |
fd4a79e7e5f0
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597 <option value="RdYlBu_r">RdYlBu reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
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598 <option value="RdYlGn_r">RdYlGn reversed</option> |
fd4a79e7e5f0
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599 <option value="YlGnBu_r">YlGnBu reversed</option> |
fd4a79e7e5f0
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600 <option value="YlOrBr_r">YlOrBr reversed</option> |
fd4a79e7e5f0
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601 <option value="YlOrRd_r">YlOrRd reversed</option> |
fd4a79e7e5f0
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602 <option value="gist_gray_r">gist_gray reversed</option> |
fd4a79e7e5f0
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603 <option value="gist_stern_r">gist_stern reversed</option> |
fd4a79e7e5f0
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604 <option value="gist_earth_r">gist_earth reversed</option> |
fd4a79e7e5f0
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605 <option value="gist_yarg_r">gist_yarg reversed</option> |
fd4a79e7e5f0
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changeset
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606 <option value="gist_ncar_r">gist_ncar reversed</option> |
fd4a79e7e5f0
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607 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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|
608 <option value="gist_heat_r">gist_heat reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
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609 <option value="gnuplot_r">gnuplot reversed</option> |
fd4a79e7e5f0
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|
610 <option value="gnuplot2_r">gnuplot2 reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
611 <option value="CMRmap_r">CMRmap reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
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612 <option value="bwr_r">bwr reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
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613 <option value="hsv_r">hsv reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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614 <option value="brg_r">brg reversed</option> |
fd4a79e7e5f0
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changeset
|
615 <option value="jet_r">jet reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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|
616 <option value="afmhot_r">afmhot reversed</option> |
fd4a79e7e5f0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
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changeset
|
617 </param> |
fd4a79e7e5f0
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|
618 |
fd4a79e7e5f0
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|
619 </xml> |
fd4a79e7e5f0
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|
620 |
fd4a79e7e5f0
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|
621 </macros> |