Mercurial > repos > bgruening > deeptools_plot_pca
annotate deepTools_macros.xml @ 8:c74dd623b281 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
author | bgruening |
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date | Wed, 23 Dec 2015 14:43:17 -0500 |
parents | 4bd03b1a8da7 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-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 e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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2 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-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 e1fd513c18e0d5b53071d99f539ac3509ced01aa-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 e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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8 </param> |
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9 <when value="no" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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10 <when value="yes"> |
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11 <yield/> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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12 </when> |
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13 </conditional> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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14 </xml> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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15 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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16 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> |
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17 #if $advancedOpt.doExtendCustom.doExtend == 'custom': |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
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18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
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19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes': |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
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20 --extendReads |
1f9a7501bd38
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
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21 #end if |
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22 $advancedOpt.ignoreDuplicates |
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23 $advancedOpt.centerReads |
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24 #if $advancedOpt.minMappingQuality: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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25 --minMappingQuality '$advancedOpt.minMappingQuality' |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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26 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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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 e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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28 --samFlagInclude $advancedOpt.samFlagInclude |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-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 e1fd513c18e0d5b53071d99f539ac3509ced01aa-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 e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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31 --samFlagExclude $advancedOpt.samFlagExclude |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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32 #end if |
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33 </token> |
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34 |
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35 <xml name="heatmap_options"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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36 <expand macro="zMin_zMax" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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37 <expand macro="colorMap" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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38 <expand macro="plotTitle" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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39 <expand macro="plotNumbers" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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40 </xml> |
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41 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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42 <token name="@HEATMAP_OPTIONS@"> |
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43 #if str($plotting_type.zMin) != "": |
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44 --zMin $plotting_type.zMin |
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45 #end if |
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46 #if str($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 are included. The default behavior is to ignore such regions." /> |
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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 time required. 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 bases)" |
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90 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> |
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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, the matrix is split into clusters using the k-means algorithm. |
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111 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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112 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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113 run the clustering using other software."/> |
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114 </when> |
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115 <when value="none" /> |
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116 </conditional> |
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117 </when> |
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118 <when value="yes" /> |
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119 </conditional> |
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120 </xml> |
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121 |
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122 <token name="@KMEANS_CLUSTERING@"> |
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123 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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124 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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125 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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126 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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127 #end if |
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128 #end if |
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129 #end if |
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130 </token> |
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131 |
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132 <xml name="samFlags"> |
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133 <param argument="--samFlagInclude" type="integer" optional="True" value="" |
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134 label="Include reads based on the SAM flag" |
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135 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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136 <param argument="--samFlagExclude" type="integer" optional="True" value="" |
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137 label="Exclude reads based on the SAM flag" |
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138 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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139 </xml> |
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140 |
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141 <xml name="read_processing_options"> |
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142 <expand macro="extendReads" /> |
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143 <expand macro="ignoreDuplicates" /> |
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144 <expand macro="centerReads" /> |
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145 <expand macro="minMappingQuality" /> |
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146 <expand macro="samFlags" /> |
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147 </xml> |
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148 |
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149 <xml name="plotNumbers"> |
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150 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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151 label="Plot the correlation value" |
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152 help="If set, then the correlation number is plotted on top of the heatmap."/> |
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153 </xml> |
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154 |
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155 <xml name="extendReads"> |
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156 <conditional name="doExtendCustom"> |
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157 <param name="doExtend" type="select" label="Extend reads to the given average fragment size." |
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158 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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159 By default *each* read mate is extended. |
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160 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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161 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. |
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162 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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163 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> |
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164 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> |
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165 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> |
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166 <option value="custom">A custom length, which will be applied to ALL reads.</option> |
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167 </param> |
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168 <when value="no" /> |
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169 <when value="yes" /> |
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170 <when value="custom"> |
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171 <param name="extendReadsValue" type="integer" value="300" min="1" |
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172 label="Extend reads to the given average fragment size" |
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173 help="Extend all reads to this length" /> |
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174 </when> |
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175 </conditional> |
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176 </xml> |
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177 |
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178 <xml name="corMethod"> |
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179 <param argument="--corMethod" type="select" label="Correlation method"> |
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180 <option value="spearman" selected="True">Spearman</option> |
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181 <option value="pearson">Pearson</option> |
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182 </param> |
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183 </xml> |
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184 |
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185 <xml name="distanceBetweenBins"> |
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186 <param argument="--distanceBetweenBins" type="integer" value="0" min="0" |
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187 label="Distance between bins" |
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188 help="By default, bamCorrelate considers consecutive bins of |
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189 the specified 'Bin size'. However, to reduce the |
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190 computation time, a larger distance between bins can |
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191 be given. Larger distances result in fewer bins being |
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192 considered."/> |
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193 </xml> |
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194 |
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195 <xml name="centerReads"> |
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196 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" |
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197 label="Center regions with respect to the fragment length" |
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198 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/> |
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199 </xml> |
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200 |
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201 <xml name="ignoreDuplicates"> |
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202 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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203 label="Ignore duplicates" |
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204 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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205 </xml> |
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206 |
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207 <xml name="sortUsing"> |
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208 <param argument="--sortUsing" type="select" label="Method used for sorting" |
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209 help="For each row the method is computed."> |
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210 <option value="mean" selected="true">mean</option> |
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211 <option value="median">median</option> |
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212 <option value="min">min</option> |
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213 <option value="max">max</option> |
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214 <option value="sum">sum</option> |
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215 <option value="region_length">region length</option> |
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216 </param> |
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217 </xml> |
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218 |
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219 <xml name="sortRegions"> |
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220 <param argument="--sortRegions" type="select" label="Sort regions" |
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221 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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222 <option value="no">no ordering</option> |
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223 <option value="descend" selected="true">descending order</option> |
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224 <option value="ascend">ascending order</option> |
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225 </param> |
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226 </xml> |
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227 |
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228 <xml name="minMappingQuality"> |
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229 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1" |
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230 label="Minimum mapping quality" |
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231 help= "If set, only reads with a mapping quality score higher than this value are considered."/> |
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232 </xml> |
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233 |
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234 <xml name="skipZeros"> |
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235 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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236 label ="Skip zeros" |
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237 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." /> |
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238 </xml> |
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239 |
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240 <xml name="fragmentLength"> |
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241 <param argument="--fragmentLength" type="integer" value="300" min="1" |
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242 label="Fragment length used for the sequencing" |
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243 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/> |
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244 </xml> |
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245 |
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246 <xml name="scaleFactor"> |
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247 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" |
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248 help="When used in combination with --normalizeTo1x or |
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249 --normalizeUsingRPKM, the computed scaling factor will |
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250 be multiplied by the given scale factor." /> |
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251 </xml> |
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252 |
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253 <xml name="scaleFactors"> |
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254 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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255 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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256 </xml> |
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257 |
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258 <xml name="stdio"> |
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259 <stdio> |
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260 <exit_code range="1:" /> |
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261 <exit_code range=":-1" /> |
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262 <regex match="Error:" /> |
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263 <regex match="Exception:" /> |
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264 <regex match="EXception:" /> |
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265 <regex match="Traceback" /> |
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266 </stdio> |
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267 </xml> |
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268 |
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269 <xml name="pseudocount"> |
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270 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
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271 </xml> |
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272 |
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273 <token name="@REFERENCES@"> |
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274 |
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275 .. class:: infomark |
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276 |
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277 For more information on the tools, please visit our `help site`_. |
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278 |
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279 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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280 |
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281 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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282 |
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283 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac |
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284 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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285 .. _help site: https://deeptools.readthedocs.org/ |
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286 |
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287 </token> |
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288 <xml name="citations"> |
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289 <citations> |
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290 <citation type="doi">10.1093/nar/gku365</citation> |
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291 <yield /> |
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292 </citations> |
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293 </xml> |
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294 |
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295 <xml name="multiple_input_bams"> |
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296 <param argument="--bamfiles" type="data" format="bam" min="2" |
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297 label="Bam file" multiple="true" |
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298 help="The BAM file must be sorted."/> |
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299 </xml> |
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300 |
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301 <xml name="multiple_input_bigwigs"> |
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302 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" |
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303 label="Bigwig file" |
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304 help="A Bigwig file."/> |
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305 </xml> |
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306 |
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307 <xml name="plotTitle"> |
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308 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
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309 label="Title of the plot" |
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310 help="Title of the plot, to be printed on top of the generated image." /> |
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311 </xml> |
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312 |
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313 <token name="@multiple_input_bams@"> |
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314 <![CDATA[ |
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315 #set files=[] |
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316 #set labels=[] |
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317 #for $counter, $bamfile in enumerate($bamfiles): |
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318 ln -s "${bamfile}" "./${counter}.bam" && |
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319 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && |
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320 #silent $files.append('%s.bam' % $counter) |
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321 #silent $labels.append('%s' % ($bamfile.display_name)) |
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322 #end for |
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323 ]]> |
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324 </token> |
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325 |
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326 <token name="@multiple_input_bigwigs@"> |
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327 <![CDATA[ |
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328 #set files=[] |
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329 #set labels=[] |
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330 #for $counter, $bigwig in enumerate($bigwigfiles): |
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331 ln -s "${bigwig}" "${counter}.bw" && |
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332 #silent $files.append('%s.bw' % $counter) |
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333 #silent $labels.append('%s' % ($bigwig.display_name)) |
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334 #end for |
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335 ]]> |
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336 </token> |
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337 |
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338 <xml name="reference_genome_source"> |
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339 <conditional name="source"> |
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340 <param name="ref_source" type="select" label="Reference genome"> |
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341 <option value="cached">locally cached</option> |
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342 <option value="history">in your history</option> |
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343 </param> |
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344 <when value="cached"> |
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345 <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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346 <options from_data_table="lastz_seqs"> |
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347 <filter type="sort_by" column="1" /> |
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348 <validator type="no_options" message="No indexes are available." /> |
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349 </options> |
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350 </param> |
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351 </when> |
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352 <when value="history"> |
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353 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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354 </when> |
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355 </conditional> |
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356 </xml> |
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357 |
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358 <token name="@reference_genome_source@"> |
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359 #if $source.ref_source=="history": |
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360 --genome $source.input1 |
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361 #else: |
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362 --genome "$source.input1_2bit.fields.path" |
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363 #end if |
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364 </token> |
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365 |
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366 <xml name="effectiveGenomeSize"> |
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367 <conditional name="effectiveGenomeSize"> |
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368 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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369 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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370 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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371 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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372 <option value="93260000">ce10 (93260000)</option> |
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373 <option value="121400000">dm3 (121400000)</option> |
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374 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
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375 <option value="2150570000">mm9 (2150570000)</option> |
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376 <option value="specific">user specified</option> |
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377 </param> |
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378 <when value="specific"> |
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379 <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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380 </when> |
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381 <when value="2150570000" /> |
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382 <when value="2451960000" /> |
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383 <when value="121400000" /> |
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384 <when value="93260000" /> |
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385 </conditional> |
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386 </xml> |
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387 |
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388 <xml name="skipNAs"> |
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389 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" |
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390 label="Ignore missing data?" |
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391 help="This parameter determines if non-covered regions |
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392 (regions without overlapping reads) in a bam/bigWig file |
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393 should be skipped. The default is to treat those |
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394 regions as having a value of zero. The decision to |
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395 skip non-covered regions depends on the interpretation |
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396 of the data. Non-covered regions may represent, for |
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397 example, repetitive regions that should be ignored. |
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398 (default: False)" /> |
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399 </xml> |
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400 |
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401 <xml name="input_save_matrix_values"> |
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402 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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403 </xml> |
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404 |
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405 <xml name="input_graphic_output_settings"> |
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406 <conditional name="output" > |
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407 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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408 <option value="no" selected="true">no</option> |
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409 <option value="yes">yes</option> |
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410 </param> |
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411 <when value="no" /> |
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412 <when value="yes"> |
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413 <yield /> |
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414 <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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415 </when> |
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416 </conditional> |
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417 </xml> |
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418 |
3
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419 |
0
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420 <xml name="input_image_file_format"> |
3
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421 <param argument="--outFileFormat" type="select" label="Image file format"> |
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422 <option value="png" selected="true">png</option> |
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423 <option value="pdf">pdf</option> |
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424 <option value="svg">svg</option> |
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425 <option value="eps">eps</option> |
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426 </param> |
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427 </xml> |
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428 |
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429 <xml name="output_image_file_format"> |
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430 <data format="png" name="outFileName" label="${tool.name} image"> |
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431 <change_format> |
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432 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
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433 <when input="output.outFileFormat" value="svg" format="svg" /> |
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434 <when input="output.outFileFormat" value="eps" format="eps" /> |
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435 </change_format> |
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436 </data> |
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437 </xml> |
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438 |
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439 <xml name="output_image_file_format_not_nested"> |
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440 <data format="png" name="outFileName" label="${tool.name} image"> |
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441 <change_format> |
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442 <when input="outFileFormat" value="pdf" format="pdf" /> |
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443 <when input="outFileFormat" value="svg" format="svg" /> |
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444 <when input="outFileFormat" value="eps" format="eps" /> |
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445 </change_format> |
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446 </data> |
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447 </xml> |
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448 |
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449 <xml name="output_save_matrix_values"> |
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450 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
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451 <filter> |
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452 (( |
2
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453 output['showOutputSettings'] == 'yes' and |
0
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454 output['saveMatrix'] is True |
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455 )) |
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456 </filter> |
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457 </data> |
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458 </xml> |
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459 |
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460 <xml name="output_graphic_outputs"> |
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461 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
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462 <filter> |
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463 (( |
2
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464 output['showOutputSettings'] == 'yes' and |
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465 output['saveSortedRegions'] is True |
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466 )) |
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467 </filter> |
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468 </data> |
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469 </xml> |
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470 |
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471 <xml name="colorMap"> |
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472 <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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473 <option value="RdYlBu" selected="true">RdYlBu</option> |
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474 <option value="Accent">Accent</option> |
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475 <option value="Spectral">Spectral</option> |
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476 <option value="Set1">Set1</option> |
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477 <option value="Set2">Set2</option> |
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478 <option value="Set3">Set3</option> |
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479 <option value="Dark2">Dark2</option> |
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480 <option value="Reds">Reds</option> |
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481 <option value="Oranges">Oranges</option> |
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482 <option value="Greens">Greens</option> |
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483 <option value="Blues">Blues</option> |
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484 <option value="Greys">Greys</option> |
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485 <option value="Purples">Purples</option> |
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486 <option value="Paired">Paired</option> |
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487 <option value="Pastel1">Pastel1</option> |
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488 <option value="Pastel2">Pastel2</option> |
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489 <option value="spring">spring</option> |
a6fdea25d41f
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490 <option value="summer">summer</option> |
a6fdea25d41f
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491 <option value="autumn">autumn</option> |
a6fdea25d41f
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492 <option value="winter">winter</option> |
a6fdea25d41f
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493 <option value="hot">hot</option> |
a6fdea25d41f
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494 <option value="coolwarm">coolwarm</option> |
a6fdea25d41f
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495 <option value="cool">cool</option> |
a6fdea25d41f
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496 <option value="seismic">seismic</option> |
a6fdea25d41f
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497 <option value="terrain">terrain</option> |
a6fdea25d41f
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498 <option value="ocean">ocean</option> |
a6fdea25d41f
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499 <option value="rainbow">rainbow</option> |
a6fdea25d41f
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500 <option value="bone">bone</option> |
a6fdea25d41f
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501 <option value="flag">flag</option> |
a6fdea25d41f
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502 <option value="prism">prism</option> |
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503 <option value="cubehelix">cubehelix</option> |
a6fdea25d41f
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504 <option value="binary">binary</option> |
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505 <option value="pink">pink</option> |
a6fdea25d41f
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506 <option value="gray">gray</option> |
a6fdea25d41f
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507 <option value="copper">copper</option> |
a6fdea25d41f
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508 <option value="BrBG">BrBG</option> |
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509 <option value="BuGn">BuGn</option> |
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510 <option value="BuPu">BuPu</option> |
a6fdea25d41f
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511 <option value="GnBu">GnBu</option> |
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512 <option value="OrRd">OrRd</option> |
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513 <option value="PiYG">PiYG</option> |
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514 <option value="PRGn">PRGn</option> |
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515 <option value="PuOr">PuOr</option> |
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516 <option value="PuRd">PuRd</option> |
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517 <option value="PuBu">PuBu</option> |
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518 <option value="RdBu">RdBu</option> |
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519 <option value="RdGy">RdGy</option> |
a6fdea25d41f
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520 <option value="RdPu">RdPu</option> |
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521 <option value="YlGn">YlGn</option> |
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522 <option value="PuBuGn">PuBuGn</option> |
a6fdea25d41f
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523 <option value="RdYlGn">RdYlGn</option> |
a6fdea25d41f
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524 <option value="YlGnBu">YlGnBu</option> |
a6fdea25d41f
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525 <option value="YlOrBr">YlOrBr</option> |
a6fdea25d41f
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526 <option value="YlOrRd">YlOrRd</option> |
a6fdea25d41f
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527 <option value="gist_gray">gist_gray</option> |
a6fdea25d41f
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528 <option value="gist_stern">gist_stern</option> |
a6fdea25d41f
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529 <option value="gist_earth">gist_earth</option> |
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530 <option value="gist_yarg">gist_yarg</option> |
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531 <option value="gist_ncar">gist_ncar</option> |
a6fdea25d41f
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532 <option value="gist_rainbow">gist_rainbow</option> |
a6fdea25d41f
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533 <option value="gist_heat">gist_heat</option> |
a6fdea25d41f
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534 <option value="gnuplot">gnuplot</option> |
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535 <option value="gnuplot2">gnuplot2</option> |
a6fdea25d41f
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536 <option value="CMRmap">CMRmap</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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537 <option value="bwr">bwr</option> |
a6fdea25d41f
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|
538 <option value="hsv">hsv</option> |
a6fdea25d41f
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539 <option value="brg">brg</option> |
a6fdea25d41f
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540 <option value="jet">jet</option> |
a6fdea25d41f
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541 <option value="afmhot">afmhot</option> |
a6fdea25d41f
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542 <option value="Accent_r">Accent reversed</option> |
a6fdea25d41f
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|
543 <option value="Spectral_r">Spectral reversed</option> |
a6fdea25d41f
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544 <option value="Set1_r">Set1 reversed</option> |
a6fdea25d41f
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545 <option value="Set2_r">Set2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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546 <option value="Set3_r">Set3 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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547 <option value="Dark2_r">Dark2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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548 <option value="Reds_r">Reds reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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549 <option value="Oranges_r">Oranges reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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550 <option value="Greens_r">Greens reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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551 <option value="Blues_r">Blues reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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552 <option value="Greys_r">Greys reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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553 <option value="Purples_r">Purples reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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554 <option value="Paired_r">Paired reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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555 <option value="Pastel1_r">Pastel1 reversed</option> |
a6fdea25d41f
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556 <option value="Pastel2_r">Pastel2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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557 <option value="spring_r">spring reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
558 <option value="summer_r">summer reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
|
559 <option value="autumn_r">autumn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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560 <option value="winter_r">winter reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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561 <option value="hot_r">hot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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562 <option value="coolwarm_r">coolwarm reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
|
563 <option value="cool_r">cool reversed</option> |
a6fdea25d41f
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564 <option value="seismic_r">seismic reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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565 <option value="terrain_r">terrain reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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|
566 <option value="ocean_r">ocean reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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567 <option value="rainbow_r">rainbow reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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568 <option value="bone_r">bone reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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parents:
diff
changeset
|
569 <option value="flag_r">flag reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
|
570 <option value="prism_r">prism reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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parents:
diff
changeset
|
571 <option value="cubehelix_r">cubehelix reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
|
572 <option value="binary_r">binary reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
|
573 <option value="pink_r">pink reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
|
574 <option value="gray_r">gray reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
|
575 <option value="copper_r">copper reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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576 <option value="BrBG_r">BrBG reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
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577 <option value="BuGn_r">BuGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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578 <option value="BuPu_r">BuPu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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579 <option value="GnBu_r">GnBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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580 <option value="OrRd_r">OrRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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581 <option value="PiYG_r">PiYG reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
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582 <option value="PRGn_r">PRGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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583 <option value="PuOr_r">PuOr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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584 <option value="PuRd_r">PuRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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585 <option value="PuBu_r">PuBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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586 <option value="RdBu_r">RdBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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587 <option value="RdGy_r">RdGy reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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588 <option value="RdPu_r">RdPu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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589 <option value="YlGn_r">YlGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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590 <option value="PuBuGn_r">PuBuGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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591 <option value="RdYlBu_r">RdYlBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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592 <option value="RdYlGn_r">RdYlGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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593 <option value="YlGnBu_r">YlGnBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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594 <option value="YlOrBr_r">YlOrBr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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595 <option value="YlOrRd_r">YlOrRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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596 <option value="gist_gray_r">gist_gray reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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597 <option value="gist_stern_r">gist_stern reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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598 <option value="gist_earth_r">gist_earth reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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599 <option value="gist_yarg_r">gist_yarg reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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600 <option value="gist_ncar_r">gist_ncar reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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601 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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602 <option value="gist_heat_r">gist_heat reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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603 <option value="gnuplot_r">gnuplot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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604 <option value="gnuplot2_r">gnuplot2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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605 <option value="CMRmap_r">CMRmap reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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606 <option value="bwr_r">bwr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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607 <option value="hsv_r">hsv reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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608 <option value="brg_r">brg reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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609 <option value="jet_r">jet reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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610 <option value="afmhot_r">afmhot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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611 </param> |
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612 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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613 </xml> |
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|
614 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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615 </macros> |