Mercurial > repos > bgruening > deeptools_estimatereadfiltering
annotate deepTools_macros.xml @ 12:c72a755904a9 draft default tip
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412
author | bgruening |
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date | Wed, 27 Sep 2023 20:20:04 +0000 |
parents | bddbd9538b08 |
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ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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1 <macros> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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2 |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
12
c72a755904a9
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412
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4 <token name="@TOOL_VERSION@">3.5.4</token> |
c72a755904a9
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 4a4029b5c2e725b7cebc27217b76d23910508412
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5 <token name="@GALAXY_VERSION@">22.05</token> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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6 <xml name="requirements"> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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7 <requirements> |
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bddbd9538b08
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
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8 <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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9 <requirement type="package" version="1.9">samtools</requirement> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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10 </requirements> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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11 <expand macro="stdio" /> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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12 <version_command>@BINARY@ --version</version_command> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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13 </xml> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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14 |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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15 <xml name="advancedOpt_scaffold"> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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16 <conditional name="advancedOpt"> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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17 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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18 <option value="no" selected="true">no</option> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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19 <option value="yes">yes</option> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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20 </param> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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21 <when value="no" /> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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22 <when value="yes"> |
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23 <yield/> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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24 </when> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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25 </conditional> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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26 </xml> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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27 |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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28 <token name="@PLOTWIDTHHEIGHT@"> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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29 --plotWidth '$advancedOpt.plotWidth' |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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30 --plotHeight '$advancedOpt.plotHeight' |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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31 </token> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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32 |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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33 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT"> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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34 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0" |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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35 label="Plot height" |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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36 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." /> |
ab078f1d0623
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37 |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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38 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0" |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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39 label="Plot width" |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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40 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." /> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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41 </xml> |
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42 |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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43 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> |
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44 #if $advancedOpt.doExtendCustom.doExtend == 'custom': |
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45 --extendReads $advancedOpt.doExtendCustom.extendReadsValue |
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46 #else if $advancedOpt.doExtendCustom.doExtend == 'yes': |
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47 --extendReads |
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48 #end if |
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49 $advancedOpt.ignoreDuplicates |
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50 $advancedOpt.centerReads |
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51 #if $advancedOpt.minMappingQuality: |
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52 --minMappingQuality '$advancedOpt.minMappingQuality' |
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53 #end if |
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54 #if $advancedOpt.samFlagInclude: |
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55 --samFlagInclude $advancedOpt.samFlagInclude |
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56 #end if |
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57 #if $advancedOpt.samFlagExclude: |
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58 --samFlagExclude $advancedOpt.samFlagExclude |
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59 #end if |
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60 #if $advancedOpt.minFragmentLength: |
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61 --minFragmentLength $advancedOpt.minFragmentLength |
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62 #end if |
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63 #if $advancedOpt.maxFragmentLength: |
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64 --maxFragmentLength $advancedOpt.maxFragmentLength |
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65 #end if |
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66 </token> |
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67 |
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68 <token name="@ADVANCED_OPTS_GTF@"> |
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69 $advancedOpt.metagene |
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70 #if $advancedOpt.transcriptID: |
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71 --transcriptID $advancedOpt.transcriptID |
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72 #end if |
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73 #if $advancedOpt.exonID: |
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74 --exonID $advancedOpt.exonID |
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75 #end if |
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76 #if $advancedOpt.transcript_id_designator: |
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77 --transcript_id_designator $advancedOpt.transcript_id_designator |
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78 #end if |
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79 </token> |
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80 |
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81 <xml name="heatmap_options"> |
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82 <expand macro="zMin_zMax" /> |
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83 <expand macro="colorMap" /> |
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84 <expand macro="plotTitle" /> |
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85 <expand macro="plotNumbers" /> |
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86 </xml> |
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87 |
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88 <token name="@HEATMAP_OPTIONS@"> |
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89 #if str($plotting_type.zMin) != "": |
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90 --zMin $plotting_type.zMin |
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91 #end if |
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92 #if str($plotting_type.zMax) != "": |
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93 --zMax $plotting_type.zMax |
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94 #end if |
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95 --colorMap '$plotting_type.colorMap' |
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96 $plotting_type.plotNumbers |
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97 --plotTitle '$plotting_type.plotTitle' |
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98 </token> |
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99 |
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100 |
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101 <xml name="includeZeros"> |
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102 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
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103 label="Include zeros" |
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104 help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." /> |
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105 </xml> |
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106 |
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107 <xml name="zMin_zMax"> |
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108 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities" |
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109 help="If not specified the value is set automatically."/> |
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110 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities" |
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111 help="If not specified the value is set automatically."/> |
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112 </xml> |
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113 |
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114 <xml name="region_limit_operation"> |
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115 <param argument="--region" type="text" value="" |
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116 label="Region of the genome to limit the operation to" |
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117 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"."> |
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118 <sanitizer> |
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119 <valid initial="string.letters,string.digits"> |
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120 <add value="|"/> |
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121 <add value=":"/> |
2
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122 <add value="."/> |
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123 </valid> |
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124 </sanitizer> |
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125 </param> |
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126 </xml> |
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127 |
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128 <xml name="smoothLength"> |
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129 <param argument="--smoothLength" type="integer" value="" optional="True" min="1" |
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130 label="Smooth values using the following length (in bases)" |
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131 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> |
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132 </xml> |
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133 |
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134 |
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135 <xml name="kmeans_clustering"> |
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136 <conditional name="used_multiple_regions"> |
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137 <param name="used_multiple_regions_options" type="select" |
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138 label="Did you compute the matrix with more than one groups of regions?" |
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139 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> |
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140 <option value="yes">Yes, I used multiple groups of regions</option> |
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141 <option value="no">No, I used only one group</option> |
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142 </param> |
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143 <when value="no"> |
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144 <conditional name="clustering"> |
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145 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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146 <option value="none">No clustering</option> |
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147 <option value="kmeans">Kmeans clustering</option> |
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148 <option value="hclust">Hierarchical clustering</option> |
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149 </param> |
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150 <when value="kmeans"> |
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151 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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152 help="When this option is set, the matrix is split into clusters using the k-means algorithm. |
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153 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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154 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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155 run the clustering using other software."/> |
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156 </when> |
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157 <when value="hclust"> |
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158 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." |
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159 help="WARNING: This option causes the tool to run for a very long time! When this option is |
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160 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. |
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161 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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162 Note that you must have used the '--missingDataAsZero' option within computeMatrix! |
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163 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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164 run the clustering using other software."/> |
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165 </when> |
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166 <when value="none" /> |
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167 </conditional> |
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168 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue="" |
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169 label="Compute the silhouette score for each region" |
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170 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed. |
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171 The silhouette score is a measure of how similar a region is to other regions in the same cluster as |
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172 opposed to those in other clusters. It will be reported in the final column of the BED file with regions. |
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173 The silhouette evaluation can be very slow when you have more than 100 000 regions." /> |
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174 </when> |
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175 <when value="yes" /> |
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176 </conditional> |
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177 </xml> |
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178 |
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179 <token name="@KMEANS_CLUSTERING@"> |
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180 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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181 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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182 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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183 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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184 #end if |
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185 #end if |
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186 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': |
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187 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: |
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188 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust |
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189 #end if |
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190 #end if |
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191 $advancedOpt.used_multiple_regions.silhouette |
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192 #end if |
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193 </token> |
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194 |
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195 <xml name="samFlags"> |
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196 <param argument="--samFlagInclude" type="integer" optional="True" value="" |
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197 label="Include reads based on the SAM flag" |
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198 help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/> |
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199 <param argument="--samFlagExclude" type="integer" optional="True" value="" |
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200 label="Exclude reads based on the SAM flag" |
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201 help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/> |
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202 </xml> |
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203 |
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204 <xml name="fragLength"> |
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205 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0" |
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206 label="Minimum fragment length for inclusion." |
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207 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." /> |
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208 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0" |
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209 label="Maximum fragment length for inclusion." |
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210 help="A value of 0 (the default) is equivalent to no maximum." /> |
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211 </xml> |
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212 |
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213 <xml name="read_processing_options"> |
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214 <expand macro="extendReads" /> |
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215 <expand macro="ignoreDuplicates" /> |
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216 <expand macro="centerReads" /> |
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217 <expand macro="minMappingQuality" /> |
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218 <expand macro="samFlags" /> |
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219 <expand macro="fragLength" /> |
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220 </xml> |
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221 |
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222 <xml name="gtf_options"> |
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223 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue="" |
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224 label="Use a metagene model" |
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225 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." /> |
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226 <param argument="--transcriptID" optional="True" value="transcript" type="text" |
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227 label="transcript designator" |
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228 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" /> |
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229 <param argument="--exonID" optional="True" value="exon" type="text" |
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230 label="exon designator" |
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231 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" /> |
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232 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" |
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233 label="transcriptID key designator" |
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234 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists) |
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235 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g., |
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236 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be |
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237 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" /> |
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238 </xml> |
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239 |
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240 |
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241 <xml name="plotNumbers"> |
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242 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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243 label="Plot the correlation value" |
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244 help="If set, then the correlation number is plotted on top of the heatmap."/> |
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245 </xml> |
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246 |
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247 <xml name="extendReads"> |
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248 <conditional name="doExtendCustom"> |
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249 <param name="doExtend" type="select" label="Extend reads to the given average fragment size." |
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250 help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size. |
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251 By default *each* read mate is extended. |
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252 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. |
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253 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. |
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254 Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not |
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255 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> |
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256 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> |
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257 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> |
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258 <option value="custom">A custom length, which will be applied to ALL reads.</option> |
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259 </param> |
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260 <when value="no" /> |
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261 <when value="yes" /> |
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262 <when value="custom"> |
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263 <param name="extendReadsValue" type="integer" value="300" min="1" |
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264 label="Extend reads to the given average fragment size" |
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265 help="Extend all reads to this length" /> |
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266 </when> |
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267 </conditional> |
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268 </xml> |
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269 |
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270 <xml name="corMethod"> |
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271 <param argument="--corMethod" type="select" label="Correlation method"> |
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272 <option value="spearman" selected="True">Spearman</option> |
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273 <option value="pearson">Pearson</option> |
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274 </param> |
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275 </xml> |
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276 |
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277 <xml name="distanceBetweenBins"> |
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278 <param argument="--distanceBetweenBins" type="integer" value="0" min="0" |
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279 label="Distance between bins" |
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280 help="By default, multiBamSummary considers consecutive bins of |
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281 the specified 'Bin size'. However, to reduce the |
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282 computation time, a larger distance between bins can |
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283 be given. Larger distances result in fewer bins being |
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284 considered."/> |
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285 </xml> |
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286 |
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287 <xml name="centerReads"> |
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288 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" |
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289 label="Center regions with respect to the fragment length" |
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290 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/> |
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291 </xml> |
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292 |
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293 <xml name="ignoreDuplicates"> |
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294 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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295 label="Ignore duplicates" |
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296 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> |
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297 </xml> |
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298 |
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299 <xml name="sortUsing"> |
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300 <param argument="--sortUsing" type="select" label="Method used for sorting" |
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301 help="For each row the method is computed."> |
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302 <option value="mean" selected="true">mean</option> |
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303 <option value="median">median</option> |
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304 <option value="min">min</option> |
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305 <option value="max">max</option> |
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306 <option value="sum">sum</option> |
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307 <option value="region_length">region length</option> |
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308 </param> |
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309 </xml> |
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310 |
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311 <xml name="sortRegionsComputeMatrix"> |
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312 <param argument="--sortRegions" type="select" label="Sort regions" |
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313 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> |
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314 <option value="no">no ordering</option> |
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315 <option value="keep" selected="true">maintain the same ordering as the input files</option> |
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316 <option value="descend">descending order</option> |
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317 <option value="ascend">ascending order</option> |
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318 </param> |
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319 </xml> |
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320 |
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321 <xml name="sortRegions"> |
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322 <param argument="--sortRegions" type="select" label="Sort regions" |
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323 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> |
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324 <option value="no">maintain the same ordering as the input files</option> |
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325 <option value="descend" selected="true">descending order</option> |
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326 <option value="ascend">ascending order</option> |
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327 </param> |
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328 </xml> |
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329 |
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330 <xml name="minMappingQuality"> |
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331 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0" |
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332 label="Minimum mapping quality" |
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333 help= "If set, only reads with a mapping quality score at least this high are considered."/> |
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334 </xml> |
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335 |
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336 <xml name="skipZeros"> |
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337 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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338 label ="Skip zeros" |
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339 help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." /> |
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340 </xml> |
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341 |
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342 <xml name="fragmentLength"> |
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343 <param argument="--fragmentLength" type="integer" min="1" optional="true" |
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344 label="Fragment length used for the sequencing" |
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345 help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/> |
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346 </xml> |
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347 |
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348 <xml name="scaleFactor"> |
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349 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" |
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350 help="The computed scaling factor will be multiplied by this (default 1)." /> |
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351 </xml> |
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352 |
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353 <xml name="scaleFactors"> |
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354 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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355 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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356 </xml> |
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357 |
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358 <xml name="stdio"> |
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359 <stdio> |
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360 <exit_code range="1:" /> |
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361 <exit_code range=":-1" /> |
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362 <regex match="Error:" /> |
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363 <regex match="Exception:" /> |
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364 <regex match="EXception:" /> |
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365 <regex match="Traceback" /> |
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366 </stdio> |
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367 </xml> |
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368 |
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369 <xml name="pseudocount"> |
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370 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/> |
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371 </xml> |
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372 <token name="@REFERENCES@"> |
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373 |
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374 .. class:: infomark |
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375 |
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376 For more information on the tools, please visit our `help site`_. |
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377 |
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378 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_. |
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379 |
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380 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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381 |
9
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382 .. _Biostars: http://biostars.org |
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383 .. _on github: http://github.com |
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384 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac |
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385 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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386 .. _help site: https://deeptools.readthedocs.org/ |
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387 |
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388 </token> |
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389 <xml name="citations"> |
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390 <citations> |
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391 <citation type="doi">10.1093/nar/gkw257</citation> |
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392 <yield /> |
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393 </citations> |
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394 </xml> |
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395 |
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396 <xml name="multiple_input_bams" tokens="MIN"> |
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397 <conditional name="multibam_conditional"> |
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398 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> |
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399 <option value="No" selected="true">No</option> |
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400 <option value="Yes">Yes</option> |
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401 </param> |
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402 <when value="No"> |
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403 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@" |
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404 label="BAM/CRAM file" multiple="true" |
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405 help=""/> |
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406 </when> |
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407 <when value="Yes"> |
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408 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files"> |
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409 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" /> |
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410 </repeat> |
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411 </when> |
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412 </conditional> |
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413 </xml> |
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414 |
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415 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE"> |
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416 <conditional name="multibigwig_conditional"> |
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417 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples |
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418 is vital to you, select Yes below."> |
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419 <option value="No" selected="true">No</option> |
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420 <option value="Yes">Yes</option> |
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421 </param> |
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422 <when value="No"> |
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423 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@" |
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424 label="@LABEL@" |
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425 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/> |
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426 </when> |
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427 <when value="Yes"> |
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428 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@"> |
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429 <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/> |
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430 </repeat> |
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431 </when> |
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432 </conditional> |
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433 </xml> |
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434 |
5
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435 <xml name="custom_sample_labels"> |
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436 <conditional name="custom_sample_labels_conditional"> |
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437 <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used."> |
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438 <option value="No" selected="true">No, use sample names in the history</option> |
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439 <option value="Yes">Yes, I want to specify new labels</option> |
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440 </param> |
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441 <when value="No"> |
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442 </when> |
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443 <when value="Yes"> |
12
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444 <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., 'sample 1'; 'sample 2')"> |
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445 <sanitizer> |
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446 <valid initial="string.letters,string.digits,string.whitespace"> |
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447 <add value="'" /> |
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448 <add value="_" /> |
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449 </valid> |
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450 </sanitizer> |
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451 <validator type="regex">[A-Za-z0-9 =-_/+]+</validator> |
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452 </param> |
5
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453 </when> |
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454 </conditional> |
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455 </xml> |
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456 |
0
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457 <xml name="plotTitle"> |
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458 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
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459 label="Title of the plot" |
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460 help="Title of the plot, to be printed on top of the generated image." /> |
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461 </xml> |
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462 |
5
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463 <xml name="legendLocation"> |
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464 <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile."> |
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465 <option value="best" selected="true">Best (automatic)</option> |
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466 <option value="upper-right">upper-right</option> |
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467 <option value="upper-left">upper-left</option> |
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468 <option value="upper-center">upper-center</option> |
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469 <option value="lower-right">lower-right</option> |
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470 <option value="lower-left">lower-left</option> |
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471 <option value="lower-center">lower-center</option> |
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472 <option value="center-right">center-right</option> |
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473 <option value="center-left">center-left</option> |
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474 <option value="center">center</option> |
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475 <option value="none">none (only works for heatmaps</option> |
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476 </param> |
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477 </xml> |
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478 |
0
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479 <xml name="labelRotation"> |
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480 <param argument="--labelRotation" type="integer" value="0" |
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481 label="Rotation of the X-axis labels (in degrees)" |
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482 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." /> |
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483 </xml> |
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484 |
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485 |
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486 <token name="@multiple_input_bams@"> |
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487 <![CDATA[ |
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488 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": |
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489 #set custom_labels=$custom_sample_labels_conditional.labels |
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490 #end if |
0
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491 #set files=[] |
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492 #set labels=[] |
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493 #import re |
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494 #if $multibam_conditional.orderMatters == "No": |
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495 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): |
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496 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) |
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497 ln -s '${bamfile}' './${counter}.bam' && |
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498 #if $bamfile.ext == 'bam': |
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499 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && |
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500 #else: |
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501 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && |
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502 #end if |
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503 #silent $files.append("'%s.bam'" % $counter) |
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504 #silent $labels.append("'%s'" % $identifier) |
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505 #end for |
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506 #else: |
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507 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): |
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508 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) |
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509 ln -s '${f.bamfiles}' './${counter}.bam' && |
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510 #if $f.bamfiles.ext == 'bam': |
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511 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' && |
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512 #else: |
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513 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' && |
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514 #end if |
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515 #silent $files.append("'%s.bam'" % $counter) |
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516 #silent $labels.append("'%s'" % $identifier) |
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517 #end for |
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518 #end if |
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519 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": |
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520 #set labels=custom_labels |
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521 #end if |
0
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522 ]]> |
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523 </token> |
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524 |
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525 <token name="@multiple_input_bigwigs@"> |
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526 <![CDATA[ |
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527 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": |
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528 #set custom_labels=$custom_sample_labels_conditional.labels |
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529 #end if |
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530 #set files=[] |
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531 #set labels=[] |
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532 #import re |
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533 #if $multibigwig_conditional.orderMatters == "No": |
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534 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): |
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535 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) |
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536 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' && |
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537 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) |
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538 #silent $labels.append("'%s'" % $identifier) |
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539 #end for |
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540 #else: |
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541 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): |
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542 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) |
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543 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' && |
0
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544 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) |
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545 #silent $labels.append("'%s'" % $identifier) |
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546 #end for |
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547 #end if |
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548 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": |
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549 #set labels=custom_labels |
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550 #end if |
0
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551 ]]> |
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552 </token> |
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553 |
ab078f1d0623
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554 <xml name="blacklist"> |
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555 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0" |
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556 label="Blacklisted regions in BED/GTF format" |
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557 help="One or more files containing regions to exclude from the analysis" /> |
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558 </xml> |
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559 |
ab078f1d0623
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560 <token name="@blacklist@"> |
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561 <![CDATA[ |
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562 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None': |
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563 #set blfiles=[] |
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564 #for $f in $advancedOpt.blackListFileName: |
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565 #silent $blfiles.append("'%s'" % $f) |
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566 #end for |
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567 #if $blfiles != ["'None'"]: |
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568 --blackListFileName #echo ' '.join($blfiles)# |
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569 #end if |
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570 #end if |
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571 ]]> |
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572 </token> |
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573 |
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574 <xml name="multiple_bed"> |
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575 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true" |
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576 label="Regions in BED/GTF format" |
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577 help="One or more files containing regions to include in the analysis" /> |
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578 </xml> |
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579 |
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580 <token name="@multiple_bed@"> |
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581 <![CDATA[ |
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582 #set files=[] |
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583 #set labels=[] |
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584 #for $f in $BED: |
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585 #silent $files.append("'%s'" % $f) |
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586 #silent $labels.append("'%s'" % $f.display_name) |
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587 #end for |
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588 #if len($files) > 0: |
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589 --BED #echo ' '.join($files)# |
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590 --regionLabels #echo ' '.join($labels)# |
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591 #end if |
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592 ]]> |
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593 </token> |
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594 |
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595 <xml name="reference_genome_source"> |
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596 <conditional name="source"> |
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597 <param name="ref_source" type="select" label="Reference genome"> |
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598 <option value="cached">locally cached</option> |
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599 <option value="history">in your history</option> |
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600 </param> |
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601 <when value="cached"> |
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602 <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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603 <options from_data_table="lastz_seqs"> |
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604 <filter type="sort_by" column="1" /> |
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605 <validator type="no_options" message="No indexes are available." /> |
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606 </options> |
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607 </param> |
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608 </when> |
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609 <when value="history"> |
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610 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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611 </when> |
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612 </conditional> |
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613 </xml> |
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614 |
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615 <token name="@reference_genome_source@"> |
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616 #if $source.ref_source=="history": |
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617 --genome $source.input1 |
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618 #else: |
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619 --genome '$source.input1_2bit.fields.path' |
0
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620 #end if |
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621 </token> |
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622 |
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623 <xml name="effectiveGenomeSize"> |
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624 <conditional name="effectiveGenomeSize"> |
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625 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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626 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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627 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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628 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html"> |
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629 <option value="93260000">ce10 (93260000)</option> |
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630 <option value="130428560">dm3 (130428560)</option> |
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631 <option value="125464728">dm6 (125464728)</option> |
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632 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option> |
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633 <option value="2701495761">GRCh38/hg38 (2701495761)</option> |
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634 <option value="2304947926">GRCm37/mm9 (2304947926)</option> |
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635 <option value="2308125349">GRCm38/mm10 (2308125349)</option> |
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636 <option value="specific">user specified</option> |
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637 </param> |
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638 <when value="specific"> |
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639 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" |
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640 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/> |
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641 </when> |
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642 <when value="93260000" /> |
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643 <when value="130428560" /> |
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644 <when value="125464728" /> |
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645 <when value="2685511504" /> |
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646 <when value="2701495761" /> |
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647 <when value="2304947926" /> |
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648 <when value="2308125349" /> |
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649 </conditional> |
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650 </xml> |
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651 |
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652 <xml name="skipNAs"> |
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653 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" |
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654 label="Ignore missing data?" |
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655 help="This parameter determines if non-covered regions |
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656 (regions without overlapping reads) in a bam/bigWig file |
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657 should be skipped. The default is to treat those |
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658 regions as having a value of zero. The decision to |
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659 skip non-covered regions depends on the interpretation |
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660 of the data. Non-covered regions may represent, for |
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661 example, repetitive regions that should be ignored. |
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662 (default: False)" /> |
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663 </xml> |
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664 |
7
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665 <xml name="skipZeroOverZero"> |
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666 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage" |
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667 help="Skip bins where BOTH files lack coverage."> |
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668 <option value="" selected="true">No</option> |
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669 <option value="--skipZeroOverZero">Yes, skip them.</option> |
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670 </param> |
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671 </xml> |
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672 |
3
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673 <xml name="exactScaling"> |
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674 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False" |
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675 label="Compute an exact scaling factor" |
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676 help="Compute an exact scaling factor rather than one based on |
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677 sampled reads. This is only useful in cases where you are |
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678 filtering some alignments out AND this are both rare and |
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679 tend to clump together in the genome. In such cases the |
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680 region-based sampling employed by deepTools would produce |
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681 inaccurate scaling factors. Note that this option results |
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682 in the process taking significantly more time to complete." /> |
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683 </xml> |
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684 |
0
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685 <xml name="input_save_matrix_values"> |
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686 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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687 </xml> |
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688 |
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689 <xml name="input_graphic_output_settings"> |
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690 <conditional name="output" > |
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691 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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692 <option value="no" selected="true">no</option> |
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693 <option value="yes">yes</option> |
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694 </param> |
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695 <when value="no" /> |
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696 <when value="yes"> |
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697 <yield /> |
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698 <param name="saveSortedRegions" type="boolean" |
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699 argument="--outFileSortedRegions" |
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700 label="Save the regions after skipping zeros or min/max threshold values" |
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701 help="The order of the regions in the file follows the sorting order selected. This is useful, |
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702 for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
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703 </when> |
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704 </conditional> |
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705 </xml> |
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706 |
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707 |
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708 <xml name="input_image_file_format"> |
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709 <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported."> |
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710 <option value="png" selected="true">png</option> |
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711 <option value="pdf">pdf</option> |
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712 <option value="svg">svg</option> |
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713 <option value="eps">eps</option> |
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714 <option value="plotly">plotly</option> |
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715 </param> |
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716 </xml> |
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717 |
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718 <xml name="output_dpi"> |
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719 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True" |
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720 label="Image dpi" help=""/> |
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721 </xml> |
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722 |
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723 <xml name="output_image_file_format"> |
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724 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image"> |
0
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725 <change_format> |
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726 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
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727 <when input="output.outFileFormat" value="svg" format="svg" /> |
ab078f1d0623
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|
728 <when input="output.outFileFormat" value="eps" format="eps" /> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
729 <when input="output.outFileFormat" value="plotly" format="html" /> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
730 </change_format> |
ab078f1d0623
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|
731 </data> |
ab078f1d0623
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|
732 </xml> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
733 |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
734 <xml name="output_image_file_format_not_nested"> |
4
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3
diff
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735 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image"> |
0
ab078f1d0623
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|
736 <change_format> |
ab078f1d0623
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|
737 <when input="outFileFormat" value="pdf" format="pdf" /> |
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|
738 <when input="outFileFormat" value="svg" format="svg" /> |
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|
739 <when input="outFileFormat" value="eps" format="eps" /> |
ab078f1d0623
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|
740 <when input="outFileFormat" value="plotly" format="html" /> |
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|
741 </change_format> |
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|
742 </data> |
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|
743 </xml> |
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|
744 |
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|
745 <xml name="output_save_matrix_values"> |
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|
746 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
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|
747 <filter> |
ab078f1d0623
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|
748 (( |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
749 output['showOutputSettings'] == 'yes' and |
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|
750 output['saveMatrix'] is True |
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|
751 )) |
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|
752 </filter> |
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|
753 </data> |
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|
754 </xml> |
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|
755 |
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|
756 <xml name="output_graphic_outputs"> |
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|
757 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
ab078f1d0623
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|
758 <filter> |
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|
759 (( |
ab078f1d0623
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|
760 output['showOutputSettings'] == 'yes' and |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
761 output['saveSortedRegions'] is True |
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|
762 )) |
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|
763 </filter> |
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|
764 </data> |
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|
765 </xml> |
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|
766 |
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|
767 <xml name="colorMap"> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
768 <param name="colorMap" type="select" label="Color map to use for the heatmap" |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
769 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
770 <option value="RdYlBu" selected="true">RdYlBu</option> |
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|
771 <option value="Accent">Accent</option> |
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|
772 <option value="Spectral">Spectral</option> |
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|
773 <option value="Set1">Set1</option> |
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|
774 <option value="Set2">Set2</option> |
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|
775 <option value="Set3">Set3</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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|
776 <option value="Dark2">Dark2</option> |
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|
777 <option value="Reds">Reds</option> |
ab078f1d0623
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|
778 <option value="Oranges">Oranges</option> |
ab078f1d0623
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|
779 <option value="Greens">Greens</option> |
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|
780 <option value="Blues">Blues</option> |
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|
781 <option value="Greys">Greys</option> |
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|
782 <option value="Purples">Purples</option> |
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|
783 <option value="Paired">Paired</option> |
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|
784 <option value="Pastel1">Pastel1</option> |
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|
785 <option value="Pastel2">Pastel2</option> |
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|
786 <option value="spring">spring</option> |
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|
787 <option value="summer">summer</option> |
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788 <option value="autumn">autumn</option> |
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|
789 <option value="winter">winter</option> |
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790 <option value="hot">hot</option> |
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|
791 <option value="coolwarm">coolwarm</option> |
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|
792 <option value="cool">cool</option> |
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|
793 <option value="seismic">seismic</option> |
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|
794 <option value="terrain">terrain</option> |
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795 <option value="ocean">ocean</option> |
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796 <option value="rainbow">rainbow</option> |
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797 <option value="bone">bone</option> |
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|
798 <option value="flag">flag</option> |
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|
799 <option value="prism">prism</option> |
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|
800 <option value="cubehelix">cubehelix</option> |
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|
801 <option value="binary">binary</option> |
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changeset
|
802 <option value="pink">pink</option> |
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|
803 <option value="gray">gray</option> |
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|
804 <option value="copper">copper</option> |
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|
805 <option value="BrBG">BrBG</option> |
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|
806 <option value="BuGn">BuGn</option> |
ab078f1d0623
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|
807 <option value="BuPu">BuPu</option> |
ab078f1d0623
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|
808 <option value="GnBu">GnBu</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
809 <option value="OrRd">OrRd</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
810 <option value="PiYG">PiYG</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
811 <option value="PRGn">PRGn</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
812 <option value="PuOr">PuOr</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
813 <option value="PuRd">PuRd</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
814 <option value="PuBu">PuBu</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
815 <option value="RdBu">RdBu</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
816 <option value="RdGy">RdGy</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
817 <option value="RdPu">RdPu</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
818 <option value="YlGn">YlGn</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
819 <option value="PuBuGn">PuBuGn</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
820 <option value="RdYlGn">RdYlGn</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
821 <option value="YlGnBu">YlGnBu</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
822 <option value="YlOrBr">YlOrBr</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
823 <option value="YlOrRd">YlOrRd</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
824 <option value="gist_gray">gist_gray</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
825 <option value="gist_stern">gist_stern</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
826 <option value="gist_earth">gist_earth</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
827 <option value="gist_yarg">gist_yarg</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
828 <option value="gist_ncar">gist_ncar</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
829 <option value="gist_rainbow">gist_rainbow</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
830 <option value="gist_heat">gist_heat</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
831 <option value="gnuplot">gnuplot</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
832 <option value="gnuplot2">gnuplot2</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
833 <option value="CMRmap">CMRmap</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
834 <option value="bwr">bwr</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
835 <option value="hsv">hsv</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
836 <option value="brg">brg</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
837 <option value="jet">jet</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
838 <option value="afmhot">afmhot</option> |
9
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
839 <option value="Wistia">Wistia</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
840 <option value="cividis">cividis</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
841 <option value="icefire">icefire</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
842 <option value="inferno">inferno</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
843 <option value="magma">magma</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
844 <option value="mako">mako</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
845 <option value="nipy_spectral">nipy_spectral</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
846 <option value="plasma">plasma</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
847 <option value="rocket">rocket</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
848 <option value="tab10">tab10</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
849 <option value="tab20">tab20</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
850 <option value="tab20b">tab20b</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
851 <option value="tab20c">tab20c</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
852 <option value="twilight">twilight</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
853 <option value="twilight_shifted">twilight_shifted</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
854 <option value="viridis">viridis</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
855 <option value="vlag">vlag</option> |
0
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
856 <option value="Accent_r">Accent reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
857 <option value="Spectral_r">Spectral reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
858 <option value="Set1_r">Set1 reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
859 <option value="Set2_r">Set2 reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
860 <option value="Set3_r">Set3 reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
861 <option value="Dark2_r">Dark2 reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
862 <option value="Reds_r">Reds reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
863 <option value="Oranges_r">Oranges reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
864 <option value="Greens_r">Greens reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
865 <option value="Blues_r">Blues reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
866 <option value="Greys_r">Greys reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
867 <option value="Purples_r">Purples reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
868 <option value="Paired_r">Paired reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
869 <option value="Pastel1_r">Pastel1 reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
870 <option value="Pastel2_r">Pastel2 reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
871 <option value="spring_r">spring reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
872 <option value="summer_r">summer reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
873 <option value="autumn_r">autumn reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
874 <option value="winter_r">winter reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
875 <option value="hot_r">hot reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
876 <option value="coolwarm_r">coolwarm reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
877 <option value="cool_r">cool reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
878 <option value="seismic_r">seismic reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
879 <option value="terrain_r">terrain reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
880 <option value="ocean_r">ocean reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
881 <option value="rainbow_r">rainbow reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
882 <option value="bone_r">bone reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
883 <option value="flag_r">flag reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
884 <option value="prism_r">prism reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
885 <option value="cubehelix_r">cubehelix reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
886 <option value="binary_r">binary reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
887 <option value="pink_r">pink reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
888 <option value="gray_r">gray reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
889 <option value="copper_r">copper reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
890 <option value="BrBG_r">BrBG reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
891 <option value="BuGn_r">BuGn reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
892 <option value="BuPu_r">BuPu reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
893 <option value="GnBu_r">GnBu reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
894 <option value="OrRd_r">OrRd reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
895 <option value="PiYG_r">PiYG reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
896 <option value="PRGn_r">PRGn reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
897 <option value="PuOr_r">PuOr reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
898 <option value="PuRd_r">PuRd reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
899 <option value="PuBu_r">PuBu reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
900 <option value="RdBu_r">RdBu reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
901 <option value="RdGy_r">RdGy reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
902 <option value="RdPu_r">RdPu reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
903 <option value="YlGn_r">YlGn reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
904 <option value="PuBuGn_r">PuBuGn reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
905 <option value="RdYlBu_r">RdYlBu reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
906 <option value="RdYlGn_r">RdYlGn reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
907 <option value="YlGnBu_r">YlGnBu reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
908 <option value="YlOrBr_r">YlOrBr reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
909 <option value="YlOrRd_r">YlOrRd reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
910 <option value="gist_gray_r">gist_gray reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
911 <option value="gist_stern_r">gist_stern reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
912 <option value="gist_earth_r">gist_earth reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
913 <option value="gist_yarg_r">gist_yarg reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
914 <option value="gist_ncar_r">gist_ncar reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
915 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
916 <option value="gist_heat_r">gist_heat reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
917 <option value="gnuplot_r">gnuplot reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
918 <option value="gnuplot2_r">gnuplot2 reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
919 <option value="CMRmap_r">CMRmap reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
920 <option value="bwr_r">bwr reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
921 <option value="hsv_r">hsv reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
922 <option value="brg_r">brg reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
923 <option value="jet_r">jet reversed</option> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
924 <option value="afmhot_r">afmhot reversed</option> |
9
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
925 <option value="Wistia_r">Wistia reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
926 <option value="cividis_r">cividis reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
927 <option value="icefire_r">icefire reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
928 <option value="inferno_r">inferno reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
929 <option value="magma_r">magma reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
930 <option value="mako_r">mako reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
931 <option value="nipy_spectral_r">nipy_spectral reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
932 <option value="plasma_r">plasma reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
933 <option value="rocket_r">rocket reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
934 <option value="tab10_r">tab10 reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
935 <option value="tab20_r">tab20 reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
936 <option value="tab20b_r">tab20b reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
937 <option value="tab20c_r">tab20c reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
938 <option value="twilight_r">twilight reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
939 <option value="twilight_shifted_r">twilight_shifted reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
940 <option value="viridis_r">viridis reversed</option> |
71082dac170c
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents:
8
diff
changeset
|
941 <option value="vlag_r">vlag reversed</option> |
0
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
942 </param> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
943 |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
944 </xml> |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
945 |
ab078f1d0623
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents:
diff
changeset
|
946 </macros> |