Mercurial > repos > bgruening > deeptools_plot_pca
annotate deepTools_macros.xml @ 32:94d2a13a344d draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author | bgruening |
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date | Thu, 15 Feb 2018 04:13:20 -0500 |
parents | d4c7104427c5 |
children | dd9094f47529 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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1 <macros> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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2 |
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5150510cd7e4
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
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3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
32
94d2a13a344d
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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4 <token name="@WRAPPER_VERSION@">3.0.0</token> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
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5 <xml name="requirements"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
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6 <requirements> |
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94d2a13a344d
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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7 <requirement type="package" version="3.0.0">deeptools</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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8 <requirement type="package" version="1.7">samtools</requirement> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
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9 </requirements> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
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10 <expand macro="stdio" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
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11 <version_command>@BINARY@ --version</version_command> |
5150510cd7e4
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
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12 </xml> |
5150510cd7e4
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
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13 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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14 <xml name="advancedOpt_scaffold"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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15 <conditional name="advancedOpt"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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16 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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17 <option value="no" selected="true">no</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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18 <option value="yes">yes</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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19 </param> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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20 <when value="no" /> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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21 <when value="yes"> |
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22 <yield/> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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23 </when> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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24 </conditional> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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25 </xml> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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26 |
28
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27 <token name="@PLOTWIDTHHEIGHT@"> |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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28 --plotWidth '$advancedOpt.plotWidth' |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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29 --plotHeight '$advancedOpt.plotHeight' |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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30 </token> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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31 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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32 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT"> |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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33 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0" |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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34 label="Plot height" |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." /> |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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36 |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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37 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0" |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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38 label="Plot width" |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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39 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." /> |
beb7f689a761
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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40 </xml> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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41 |
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42 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> |
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43 #if $advancedOpt.doExtendCustom.doExtend == 'custom': |
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44 --extendReads $advancedOpt.doExtendCustom.extendReadsValue |
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45 #else if $advancedOpt.doExtendCustom.doExtend == 'yes': |
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46 --extendReads |
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47 #end if |
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48 $advancedOpt.ignoreDuplicates |
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49 $advancedOpt.centerReads |
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50 #if $advancedOpt.minMappingQuality: |
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51 --minMappingQuality '$advancedOpt.minMappingQuality' |
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52 #end if |
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53 #if $advancedOpt.samFlagInclude: |
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54 --samFlagInclude $advancedOpt.samFlagInclude |
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55 #end if |
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56 #if $advancedOpt.samFlagExclude: |
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57 --samFlagExclude $advancedOpt.samFlagExclude |
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58 #end if |
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59 #if $advancedOpt.minFragmentLength: |
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60 --minFragmentLength $advancedOpt.minFragmentLength |
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61 #end if |
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62 #if $advancedOpt.maxFragmentLength: |
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63 --maxFragmentLength $advancedOpt.maxFragmentLength |
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64 #end if |
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65 </token> |
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66 |
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67 <token name="@ADVANCED_OPTS_GTF@"> |
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68 $advancedOpt.metagene |
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69 #if $advancedOpt.transcriptID: |
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70 --transcriptID $advancedOpt.transcriptID |
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71 #end if |
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72 #if $advancedOpt.exonID: |
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73 --exonID $advancedOpt.exonID |
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74 #end if |
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75 #if $advancedOpt.transcript_id_designator: |
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76 --transcript_id_designator $advancedOpt.transcript_id_designator |
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77 #end if |
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78 </token> |
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79 |
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80 <xml name="heatmap_options"> |
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81 <expand macro="zMin_zMax" /> |
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82 <expand macro="colorMap" /> |
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83 <expand macro="plotTitle" /> |
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84 <expand macro="plotNumbers" /> |
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85 </xml> |
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86 |
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87 <token name="@HEATMAP_OPTIONS@"> |
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88 #if str($plotting_type.zMin) != "": |
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89 --zMin $plotting_type.zMin |
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90 #end if |
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91 #if str($plotting_type.zMax) != "": |
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92 --zMax $plotting_type.zMax |
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93 #end if |
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94 --colorMap '$plotting_type.colorMap' |
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95 $plotting_type.plotNumbers |
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96 --plotTitle '$plotting_type.plotTitle' |
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97 </token> |
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98 |
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99 |
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100 <xml name="includeZeros"> |
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101 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
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102 label="Include zeros" |
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103 help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." /> |
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104 </xml> |
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105 |
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106 <xml name="zMin_zMax"> |
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107 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities" |
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108 help="If not specified the value is set automatically."/> |
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109 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities" |
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110 help="If not specified the value is set automatically."/> |
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111 </xml> |
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112 |
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113 <xml name="region_limit_operation"> |
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114 <param argument="--region" type="text" value="" |
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115 label="Region of the genome to limit the operation to" |
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116 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"."> |
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117 <sanitizer> |
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118 <valid initial="string.letters,string.digits"> |
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119 <add value="|"/> |
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120 <add value=":"/> |
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121 </valid> |
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122 </sanitizer> |
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123 </param> |
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124 </xml> |
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125 |
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126 <xml name="smoothLength"> |
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127 <param argument="--smoothLength" type="integer" value="" optional="True" min="1" |
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128 label="Smooth values using the following length (in bases)" |
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129 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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130 </xml> |
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131 |
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132 |
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133 <xml name="kmeans_clustering"> |
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134 <conditional name="used_multiple_regions"> |
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135 <param name="used_multiple_regions_options" type="select" |
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136 label="Did you compute the matrix with more than one groups of regions?" |
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137 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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138 <option value="yes">Yes, I used multiple groups of regions</option> |
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139 <option value="no">No, I used only one group</option> |
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140 </param> |
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141 <when value="no"> |
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142 <conditional name="clustering"> |
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143 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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144 <option value="none">No clustering</option> |
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145 <option value="kmeans">Kmeans clustering</option> |
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146 <option value="hclust">Hierarchical clustering</option> |
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147 </param> |
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148 <when value="kmeans"> |
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149 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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150 help="When this option is set, the matrix is split into clusters using the k-means algorithm. |
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151 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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152 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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153 run the clustering using other software."/> |
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154 </when> |
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155 <when value="hclust"> |
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156 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." |
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157 help="WARNING: This option causes the tool to run for a very long time! When this option is |
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158 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. |
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159 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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160 Note that you must have used the '--missingDataAsZero' option within computeMatrix! |
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161 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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162 run the clustering using other software."/> |
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163 </when> |
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164 <when value="none" /> |
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165 </conditional> |
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166 </when> |
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167 <when value="yes" /> |
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168 </conditional> |
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169 </xml> |
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170 |
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171 <token name="@KMEANS_CLUSTERING@"> |
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172 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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173 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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174 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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175 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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176 #end if |
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177 #end if |
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178 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': |
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179 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: |
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180 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust |
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181 #end if |
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182 #end if |
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183 #end if |
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184 </token> |
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185 |
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186 <xml name="samFlags"> |
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187 <param argument="--samFlagInclude" type="integer" optional="True" value="" |
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188 label="Include reads based on the SAM flag" |
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189 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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190 <param argument="--samFlagExclude" type="integer" optional="True" value="" |
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191 label="Exclude reads based on the SAM flag" |
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192 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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193 </xml> |
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194 |
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195 <xml name="fragLength"> |
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196 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0" |
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197 label="Minimum fragment length for inclusion." |
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198 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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199 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0" |
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200 label="Maximum fragment length for inclusion." |
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201 help="A value of 0 (the default) is equivalent to no maximum." /> |
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202 </xml> |
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203 |
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204 <xml name="read_processing_options"> |
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205 <expand macro="extendReads" /> |
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206 <expand macro="ignoreDuplicates" /> |
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207 <expand macro="centerReads" /> |
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208 <expand macro="minMappingQuality" /> |
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209 <expand macro="samFlags" /> |
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210 <expand macro="fragLength" /> |
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211 </xml> |
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212 |
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213 <xml name="gtf_options"> |
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214 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue="" |
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215 label="Use a metagene model" |
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216 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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217 <param argument="--transcriptID" optional="True" value="transcript" type="text" |
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218 label="trascript designator" |
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219 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" /> |
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220 <param argument="--exonID" optional="True" value="exon" type="text" |
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221 label="exon designator" |
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222 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" /> |
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223 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" |
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224 label="transcriptID key designator" |
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225 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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226 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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227 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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228 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" /> |
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229 </xml> |
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230 |
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231 |
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232 <xml name="plotNumbers"> |
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233 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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234 label="Plot the correlation value" |
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235 help="If set, then the correlation number is plotted on top of the heatmap."/> |
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236 </xml> |
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237 |
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238 <xml name="extendReads"> |
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239 <conditional name="doExtendCustom"> |
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240 <param name="doExtend" type="select" label="Extend reads to the given average fragment size." |
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241 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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242 By default *each* read mate is extended. |
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243 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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244 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. |
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245 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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246 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> |
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247 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> |
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248 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> |
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249 <option value="custom">A custom length, which will be applied to ALL reads.</option> |
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250 </param> |
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251 <when value="no" /> |
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252 <when value="yes" /> |
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253 <when value="custom"> |
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254 <param name="extendReadsValue" type="integer" value="300" min="1" |
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255 label="Extend reads to the given average fragment size" |
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256 help="Extend all reads to this length" /> |
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257 </when> |
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258 </conditional> |
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259 </xml> |
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260 |
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261 <xml name="corMethod"> |
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262 <param argument="--corMethod" type="select" label="Correlation method"> |
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263 <option value="spearman" selected="True">Spearman</option> |
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264 <option value="pearson">Pearson</option> |
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265 </param> |
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266 </xml> |
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267 |
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268 <xml name="distanceBetweenBins"> |
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269 <param argument="--distanceBetweenBins" type="integer" value="0" min="0" |
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270 label="Distance between bins" |
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271 help="By default, multiBamSummary considers consecutive bins of |
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272 the specified 'Bin size'. However, to reduce the |
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273 computation time, a larger distance between bins can |
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274 be given. Larger distances result in fewer bins being |
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275 considered."/> |
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276 </xml> |
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277 |
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278 <xml name="centerReads"> |
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279 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" |
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280 label="Center regions with respect to the fragment length" |
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281 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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282 </xml> |
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283 |
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284 <xml name="ignoreDuplicates"> |
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285 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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286 label="Ignore duplicates" |
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287 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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288 </xml> |
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289 |
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290 <xml name="sortUsing"> |
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291 <param argument="--sortUsing" type="select" label="Method used for sorting" |
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292 help="For each row the method is computed."> |
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293 <option value="mean" selected="true">mean</option> |
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294 <option value="median">median</option> |
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295 <option value="min">min</option> |
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296 <option value="max">max</option> |
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297 <option value="sum">sum</option> |
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298 <option value="region_length">region length</option> |
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299 </param> |
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300 </xml> |
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301 |
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302 <xml name="sortRegionsComputeMatrix"> |
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303 <param argument="--sortRegions" type="select" label="Sort regions" |
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304 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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305 <option value="no">no ordering</option> |
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306 <option value="keep" selected="true">maintain the same ordering as the input files</option> |
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307 <option value="descend">descending order</option> |
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308 <option value="ascend">ascending order</option> |
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309 </param> |
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310 </xml> |
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311 |
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312 <xml name="sortRegions"> |
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313 <param argument="--sortRegions" type="select" label="Sort regions" |
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314 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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315 <option value="no">maintain the same ordering as the input files</option> |
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316 <option value="descend" selected="true">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="minMappingQuality"> |
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322 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0" |
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323 label="Minimum mapping quality" |
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324 help= "If set, only reads with a mapping quality score at least this high are considered."/> |
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325 </xml> |
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326 |
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327 <xml name="skipZeros"> |
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328 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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329 label ="Skip zeros" |
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330 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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331 </xml> |
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332 |
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333 <xml name="fragmentLength"> |
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334 <param argument="--fragmentLength" type="integer" min="1" optional="true" |
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335 label="Fragment length used for the sequencing" |
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336 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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337 </xml> |
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338 |
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339 <xml name="scaleFactor"> |
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340 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" |
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341 help="The computed scaling factor will be multiplied by this (default 1)." /> |
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342 </xml> |
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343 |
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344 <xml name="scaleFactors"> |
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345 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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346 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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347 </xml> |
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348 |
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349 <xml name="stdio"> |
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350 <stdio> |
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351 <exit_code range="1:" /> |
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352 <exit_code range=":-1" /> |
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353 <regex match="Error:" /> |
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354 <regex match="Exception:" /> |
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355 <regex match="EXception:" /> |
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356 <regex match="Traceback" /> |
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357 </stdio> |
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358 </xml> |
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359 |
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360 <xml name="pseudocount"> |
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361 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
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362 </xml> |
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363 |
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364 <token name="@REFERENCES@"> |
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365 |
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366 .. class:: infomark |
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367 |
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368 For more information on the tools, please visit our `help site`_. |
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369 |
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370 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com |
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371 |
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372 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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373 |
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374 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac |
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375 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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376 .. _help site: https://deeptools.readthedocs.org/ |
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377 |
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378 </token> |
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379 <xml name="citations"> |
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380 <citations> |
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381 <citation type="doi">10.1093/nar/gkw257</citation> |
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382 <yield /> |
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383 </citations> |
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384 </xml> |
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385 |
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386 <xml name="multiple_input_bams" tokens="MIN"> |
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387 <conditional name="multibam_conditional"> |
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388 <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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389 <option value="No" selected="true">No</option> |
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390 <option value="Yes">Yes</option> |
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391 </param> |
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392 <when value="No"> |
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393 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@" |
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394 label="BAM/CRAM file" multiple="true" |
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395 help=""/> |
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396 </when> |
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397 <when value="Yes"> |
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398 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files"> |
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399 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" /> |
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400 </repeat> |
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401 </when> |
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402 </conditional> |
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403 </xml> |
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404 |
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405 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE"> |
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406 <conditional name="multibigwig_conditional"> |
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407 <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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408 is vital to you, select Yes below."> |
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409 <option value="No" selected="true">No</option> |
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410 <option value="Yes">Yes</option> |
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411 </param> |
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412 <when value="No"> |
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413 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@" |
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414 label="@LABEL@" |
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415 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/> |
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416 </when> |
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417 <when value="Yes"> |
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418 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@"> |
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419 <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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420 </repeat> |
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421 </when> |
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422 </conditional> |
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423 </xml> |
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424 |
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425 <xml name="plotTitle"> |
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426 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
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427 label="Title of the plot" |
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428 help="Title of the plot, to be printed on top of the generated image." /> |
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429 </xml> |
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430 |
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431 <xml name="labelRotation"> |
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432 <param argument="--labelRotation" type="integer" value="0" |
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433 label="Rotation of the X-axis labels (in degrees)" |
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434 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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435 </xml> |
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436 |
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437 |
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438 <token name="@multiple_input_bams@"> |
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439 <![CDATA[ |
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440 #set files=[] |
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441 #set labels=[] |
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442 #import re |
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443 #if $multibam_conditional.orderMatters == "No": |
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444 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): |
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445 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) |
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446 ln -s "${bamfile}" "./${counter}.bam" && |
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447 #if $bamfile.ext == 'bam': |
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448 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && |
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449 #else: |
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450 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && |
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451 #end if |
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452 #silent $files.append("'%s.bam'" % $counter) |
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453 #silent $labels.append("'%s'" % identifier) |
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454 #end for |
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455 #else: |
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456 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): |
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457 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) |
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458 ln -s "${f.bamfiles}" "./${counter}.bam" && |
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459 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" && |
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460 #if $f.bamfiles.ext == 'bam': |
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461 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' && |
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462 #else: |
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463 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' && |
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464 #end if |
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465 #silent $files.append("'%s.bam'" % $counter) |
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466 #silent $labels.append("'%s'" % $identifier) |
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467 #end for |
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468 #end if |
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469 ]]> |
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470 </token> |
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471 |
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472 <token name="@multiple_input_bigwigs@"> |
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473 <![CDATA[ |
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474 #set files=[] |
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475 #set labels=[] |
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476 #import re |
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477 #if $multibigwig_conditional.orderMatters == "No": |
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478 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): |
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479 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) |
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480 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && |
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481 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) |
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482 #silent $labels.append("'%s'" % $identifier) |
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483 #end for |
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484 #else: |
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485 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): |
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486 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) |
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487 ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" && |
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488 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) |
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489 #silent $labels.append("'%s'" % $identifier) |
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490 #end for |
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491 #end if |
0
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492 ]]> |
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493 </token> |
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494 |
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495 <xml name="blacklist"> |
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496 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0" |
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497 label="Blacklisted regions in BED/GTF format" |
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498 help="One or more files containing regions to exclude from the analysis" /> |
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499 </xml> |
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500 |
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501 <token name="@blacklist@"> |
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502 <![CDATA[ |
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503 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None': |
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504 #set blfiles=[] |
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505 #for $f in $advancedOpt.blackListFileName: |
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506 #silent $blfiles.append("'%s'" % $f) |
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507 #end for |
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508 #if $blfiles != ["'None'"]: |
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509 --blackListFileName #echo ' '.join($blfiles)# |
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510 #end if |
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511 #end if |
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512 ]]> |
21
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513 </token> |
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514 |
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515 <xml name="multiple_bed"> |
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516 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true" |
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517 label="Regions in BED/GTF format" |
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518 help="One or more files containing regions to include in the analysis" /> |
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519 </xml> |
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520 |
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521 <token name="@multiple_bed@"> |
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522 <![CDATA[ |
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523 #set files=[] |
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524 #set labels=[] |
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525 #for $f in $BED: |
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526 #silent $files.append("'%s'" % $f) |
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527 #silent $labels.append("'%s'" % $f.display_name) |
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528 #end for |
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529 #if len($files) > 0: |
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530 --BED #echo ' '.join($files)# |
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531 --regionLabels #echo ' '.join($labels)# |
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532 #end if |
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533 ]]> |
21
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534 </token> |
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535 |
0
a6fdea25d41f
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536 <xml name="reference_genome_source"> |
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537 <conditional name="source"> |
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538 <param name="ref_source" type="select" label="Reference genome"> |
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539 <option value="cached">locally cached</option> |
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540 <option value="history">in your history</option> |
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541 </param> |
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542 <when value="cached"> |
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543 <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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544 <options from_data_table="lastz_seqs"> |
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545 <filter type="sort_by" column="1" /> |
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546 <validator type="no_options" message="No indexes are available." /> |
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547 </options> |
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548 </param> |
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549 </when> |
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550 <when value="history"> |
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551 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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552 </when> |
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553 </conditional> |
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554 </xml> |
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555 |
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556 <token name="@reference_genome_source@"> |
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557 #if $source.ref_source=="history": |
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558 --genome $source.input1 |
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559 #else: |
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560 --genome "$source.input1_2bit.fields.path" |
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561 #end if |
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562 </token> |
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563 |
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564 <xml name="effectiveGenomeSize"> |
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565 <conditional name="effectiveGenomeSize"> |
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566 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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567 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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568 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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569 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html"> |
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570 <option value="93260000">ce10 (93260000)</option> |
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571 <option value="130428560">dm3 (130428560)</option> |
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572 <option value="125464728">dm6 (125464728)</option> |
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573 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option> |
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574 <option value="2701495761">GRCh38/hg38 (2701495761)</option> |
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575 <option value="2304947926">GRCm37/mm9 (2304947926)</option> |
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576 <option value="2308125349">GRCm38/mm10 (2308125349)</option> |
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577 <option value="specific">user specified</option> |
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578 </param> |
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579 <when value="specific"> |
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580 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" |
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581 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/> |
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582 </when> |
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583 <when value="93260000" /> |
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584 <when value="130428560" /> |
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585 <when value="125464728" /> |
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586 <when value="2685511504" /> |
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587 <when value="2701495761" /> |
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588 <when value="2304947926" /> |
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589 <when value="2308125349" /> |
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590 </conditional> |
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591 </xml> |
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592 |
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593 <xml name="skipNAs"> |
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594 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" |
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595 label="Ignore missing data?" |
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596 help="This parameter determines if non-covered regions |
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597 (regions without overlapping reads) in a bam/bigWig file |
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598 should be skipped. The default is to treat those |
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599 regions as having a value of zero. The decision to |
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600 skip non-covered regions depends on the interpretation |
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601 of the data. Non-covered regions may represent, for |
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602 example, repetitive regions that should be ignored. |
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603 (default: False)" /> |
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604 </xml> |
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605 |
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606 <xml name="input_save_matrix_values"> |
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607 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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608 </xml> |
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609 |
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610 <xml name="input_graphic_output_settings"> |
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611 <conditional name="output" > |
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612 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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613 <option value="no" selected="true">no</option> |
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614 <option value="yes">yes</option> |
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615 </param> |
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616 <when value="no" /> |
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617 <when value="yes"> |
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618 <yield /> |
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619 <param name="saveSortedRegions" type="boolean" |
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620 argument="--outFileSortedRegions" |
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621 label="Save the regions after skipping zeros or min/max threshold values" |
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622 help="The order of the regions in the file follows the sorting order selected. This is useful, |
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623 for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
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624 </when> |
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625 </conditional> |
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626 </xml> |
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627 |
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628 |
0
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629 <xml name="input_image_file_format"> |
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630 <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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631 <option value="png" selected="true">png</option> |
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632 <option value="pdf">pdf</option> |
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633 <option value="svg">svg</option> |
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634 <option value="eps">eps</option> |
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635 <option value="plotly">plotly</option> |
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636 </param> |
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637 </xml> |
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638 |
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639 <xml name="output_dpi"> |
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640 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True" |
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641 label="Image dpi" help=""/> |
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642 </xml> |
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643 |
0
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644 <xml name="output_image_file_format"> |
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645 <data format="png" name="outFileName" label="${tool.name} image"> |
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646 <change_format> |
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647 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
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648 <when input="output.outFileFormat" value="svg" format="svg" /> |
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649 <when input="output.outFileFormat" value="eps" format="eps" /> |
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650 <when input="output.outFileFormat" value="plotly" format="html" /> |
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651 </change_format> |
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652 </data> |
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653 </xml> |
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654 |
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655 <xml name="output_image_file_format_not_nested"> |
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656 <data format="png" name="outFileName" label="${tool.name} image"> |
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657 <change_format> |
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658 <when input="outFileFormat" value="pdf" format="pdf" /> |
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659 <when input="outFileFormat" value="svg" format="svg" /> |
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660 <when input="outFileFormat" value="eps" format="eps" /> |
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661 <when input="outFileFormat" value="plotly" format="html" /> |
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662 </change_format> |
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663 </data> |
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664 </xml> |
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665 |
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666 <xml name="output_save_matrix_values"> |
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667 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
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668 <filter> |
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669 (( |
2
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670 output['showOutputSettings'] == 'yes' and |
0
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671 output['saveMatrix'] is True |
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672 )) |
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673 </filter> |
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674 </data> |
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675 </xml> |
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676 |
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677 <xml name="output_graphic_outputs"> |
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678 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
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679 <filter> |
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680 (( |
2
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681 output['showOutputSettings'] == 'yes' and |
0
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682 output['saveSortedRegions'] is True |
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683 )) |
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684 </filter> |
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685 </data> |
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686 </xml> |
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687 |
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688 <xml name="colorMap"> |
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689 <param name="colorMap" type="select" label="Color map to use for the heatmap" |
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690 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"> |
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691 <option value="RdYlBu" selected="true">RdYlBu</option> |
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692 <option value="Accent">Accent</option> |
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693 <option value="Spectral">Spectral</option> |
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694 <option value="Set1">Set1</option> |
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695 <option value="Set2">Set2</option> |
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696 <option value="Set3">Set3</option> |
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697 <option value="Dark2">Dark2</option> |
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698 <option value="Reds">Reds</option> |
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699 <option value="Oranges">Oranges</option> |
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700 <option value="Greens">Greens</option> |
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701 <option value="Blues">Blues</option> |
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702 <option value="Greys">Greys</option> |
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703 <option value="Purples">Purples</option> |
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704 <option value="Paired">Paired</option> |
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705 <option value="Pastel1">Pastel1</option> |
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706 <option value="Pastel2">Pastel2</option> |
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707 <option value="spring">spring</option> |
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708 <option value="summer">summer</option> |
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709 <option value="autumn">autumn</option> |
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710 <option value="winter">winter</option> |
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711 <option value="hot">hot</option> |
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712 <option value="coolwarm">coolwarm</option> |
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713 <option value="cool">cool</option> |
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714 <option value="seismic">seismic</option> |
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715 <option value="terrain">terrain</option> |
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716 <option value="ocean">ocean</option> |
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717 <option value="rainbow">rainbow</option> |
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718 <option value="bone">bone</option> |
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719 <option value="flag">flag</option> |
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720 <option value="prism">prism</option> |
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721 <option value="cubehelix">cubehelix</option> |
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722 <option value="binary">binary</option> |
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723 <option value="pink">pink</option> |
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724 <option value="gray">gray</option> |
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725 <option value="copper">copper</option> |
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726 <option value="BrBG">BrBG</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
727 <option value="BuGn">BuGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
728 <option value="BuPu">BuPu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
729 <option value="GnBu">GnBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
730 <option value="OrRd">OrRd</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
731 <option value="PiYG">PiYG</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
732 <option value="PRGn">PRGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
733 <option value="PuOr">PuOr</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
734 <option value="PuRd">PuRd</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
735 <option value="PuBu">PuBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
736 <option value="RdBu">RdBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
737 <option value="RdGy">RdGy</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
738 <option value="RdPu">RdPu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
739 <option value="YlGn">YlGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
740 <option value="PuBuGn">PuBuGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
741 <option value="RdYlGn">RdYlGn</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
742 <option value="YlGnBu">YlGnBu</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
743 <option value="YlOrBr">YlOrBr</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
744 <option value="YlOrRd">YlOrRd</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
745 <option value="gist_gray">gist_gray</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
746 <option value="gist_stern">gist_stern</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
747 <option value="gist_earth">gist_earth</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
748 <option value="gist_yarg">gist_yarg</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
749 <option value="gist_ncar">gist_ncar</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
750 <option value="gist_rainbow">gist_rainbow</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
751 <option value="gist_heat">gist_heat</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
752 <option value="gnuplot">gnuplot</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
753 <option value="gnuplot2">gnuplot2</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
754 <option value="CMRmap">CMRmap</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
755 <option value="bwr">bwr</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
756 <option value="hsv">hsv</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
757 <option value="brg">brg</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
758 <option value="jet">jet</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
759 <option value="afmhot">afmhot</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
760 <option value="Accent_r">Accent reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
761 <option value="Spectral_r">Spectral reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
762 <option value="Set1_r">Set1 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
763 <option value="Set2_r">Set2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
764 <option value="Set3_r">Set3 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
765 <option value="Dark2_r">Dark2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
766 <option value="Reds_r">Reds reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
767 <option value="Oranges_r">Oranges reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
768 <option value="Greens_r">Greens reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
769 <option value="Blues_r">Blues reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
770 <option value="Greys_r">Greys reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
771 <option value="Purples_r">Purples reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
772 <option value="Paired_r">Paired reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
773 <option value="Pastel1_r">Pastel1 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
774 <option value="Pastel2_r">Pastel2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
775 <option value="spring_r">spring reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
776 <option value="summer_r">summer reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
777 <option value="autumn_r">autumn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
778 <option value="winter_r">winter reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
779 <option value="hot_r">hot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
780 <option value="coolwarm_r">coolwarm reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
781 <option value="cool_r">cool reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
782 <option value="seismic_r">seismic reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
783 <option value="terrain_r">terrain reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
784 <option value="ocean_r">ocean reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
785 <option value="rainbow_r">rainbow reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
786 <option value="bone_r">bone reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
787 <option value="flag_r">flag reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
788 <option value="prism_r">prism reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
789 <option value="cubehelix_r">cubehelix reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
790 <option value="binary_r">binary reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
791 <option value="pink_r">pink reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
792 <option value="gray_r">gray reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
793 <option value="copper_r">copper reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
794 <option value="BrBG_r">BrBG reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
795 <option value="BuGn_r">BuGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
796 <option value="BuPu_r">BuPu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
797 <option value="GnBu_r">GnBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
798 <option value="OrRd_r">OrRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
799 <option value="PiYG_r">PiYG reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
800 <option value="PRGn_r">PRGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
801 <option value="PuOr_r">PuOr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
802 <option value="PuRd_r">PuRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
803 <option value="PuBu_r">PuBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
804 <option value="RdBu_r">RdBu reversed</option> |
a6fdea25d41f
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805 <option value="RdGy_r">RdGy reversed</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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806 <option value="RdPu_r">RdPu reversed</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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807 <option value="YlGn_r">YlGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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808 <option value="PuBuGn_r">PuBuGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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809 <option value="RdYlBu_r">RdYlBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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810 <option value="RdYlGn_r">RdYlGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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811 <option value="YlGnBu_r">YlGnBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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812 <option value="YlOrBr_r">YlOrBr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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813 <option value="YlOrRd_r">YlOrRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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814 <option value="gist_gray_r">gist_gray reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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815 <option value="gist_stern_r">gist_stern reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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816 <option value="gist_earth_r">gist_earth reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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817 <option value="gist_yarg_r">gist_yarg reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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818 <option value="gist_ncar_r">gist_ncar reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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819 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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820 <option value="gist_heat_r">gist_heat reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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821 <option value="gnuplot_r">gnuplot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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822 <option value="gnuplot2_r">gnuplot2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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823 <option value="CMRmap_r">CMRmap reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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824 <option value="bwr_r">bwr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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825 <option value="hsv_r">hsv reversed</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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826 <option value="brg_r">brg reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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827 <option value="jet_r">jet reversed</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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828 <option value="afmhot_r">afmhot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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829 </param> |
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830 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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831 </xml> |
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832 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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833 </macros> |