Mercurial > repos > bgruening > deeptools_bigwig_compare
annotate deepTools_macros.xml @ 22:6f1cf6c1474b draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
author | bgruening |
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date | Tue, 19 Feb 2019 09:55:45 -0500 |
parents | 17b7e83820d7 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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1 <macros> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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2 |
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efc677b291c5
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
22
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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4 <token name="@WRAPPER_VERSION@">3.2.0.0</token> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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5 <xml name="requirements"> |
efc677b291c5
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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6 <requirements> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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7 <requirement type="package" version="3.2.0">deeptools</requirement> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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8 <requirement type="package" version="1.9">samtools</requirement> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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9 </requirements> |
efc677b291c5
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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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 09975f870c75347fba5c6777c9f3b442bdeeb289
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11 <version_command>@BINARY@ --version</version_command> |
efc677b291c5
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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12 </xml> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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13 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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14 <xml name="advancedOpt_scaffold"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-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 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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16 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
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17 <option value="no" selected="true">no</option> |
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18 <option value="yes">yes</option> |
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19 </param> |
49a569aecb22
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20 <when value="no" /> |
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21 <when value="yes"> |
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22 <yield/> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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23 </when> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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24 </conditional> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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25 </xml> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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26 |
14
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27 <token name="@PLOTWIDTHHEIGHT@"> |
3b82b38fbaf3
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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28 --plotWidth '$advancedOpt.plotWidth' |
3b82b38fbaf3
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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29 --plotHeight '$advancedOpt.plotHeight' |
3b82b38fbaf3
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"> |
3b82b38fbaf3
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" |
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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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35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." /> |
3b82b38fbaf3
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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36 |
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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" |
3b82b38fbaf3
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
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38 label="Plot width" |
3b82b38fbaf3
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." /> |
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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 $advancedOpt.transcript_id_designator |
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77 #end if |
0
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78 </token> |
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79 |
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80 <xml name="heatmap_options"> |
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81 <expand macro="zMin_zMax" /> |
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82 <expand macro="colorMap" /> |
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83 <expand macro="plotTitle" /> |
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84 <expand macro="plotNumbers" /> |
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85 </xml> |
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86 |
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87 <token name="@HEATMAP_OPTIONS@"> |
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88 #if str($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 <add value="."/> |
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122 </valid> |
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123 </sanitizer> |
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124 </param> |
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125 </xml> |
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126 |
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127 <xml name="smoothLength"> |
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128 <param argument="--smoothLength" type="integer" value="" optional="True" min="1" |
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129 label="Smooth values using the following length (in bases)" |
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130 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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131 </xml> |
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132 |
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133 |
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134 <xml name="kmeans_clustering"> |
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135 <conditional name="used_multiple_regions"> |
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136 <param name="used_multiple_regions_options" type="select" |
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137 label="Did you compute the matrix with more than one groups of regions?" |
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138 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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139 <option value="yes">Yes, I used multiple groups of regions</option> |
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140 <option value="no">No, I used only one group</option> |
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141 </param> |
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142 <when value="no"> |
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143 <conditional name="clustering"> |
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144 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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145 <option value="none">No clustering</option> |
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146 <option value="kmeans">Kmeans clustering</option> |
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147 <option value="hclust">Hierarchical clustering</option> |
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148 </param> |
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149 <when value="kmeans"> |
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150 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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151 help="When this option is set, the matrix is split into clusters using the k-means algorithm. |
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152 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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153 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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154 run the clustering using other software."/> |
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155 </when> |
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156 <when value="hclust"> |
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157 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." |
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158 help="WARNING: This option causes the tool to run for a very long time! When this option is |
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159 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. |
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160 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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161 Note that you must have used the '--missingDataAsZero' option within computeMatrix! |
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162 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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163 run the clustering using other software."/> |
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164 </when> |
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165 <when value="none" /> |
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166 </conditional> |
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167 </when> |
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168 <when value="yes" /> |
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169 </conditional> |
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170 </xml> |
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171 |
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172 <token name="@KMEANS_CLUSTERING@"> |
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173 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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174 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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175 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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176 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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177 #end if |
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178 #end if |
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179 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': |
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180 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: |
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181 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust |
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182 #end if |
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183 #end if |
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184 #end if |
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185 </token> |
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186 |
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187 <xml name="samFlags"> |
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188 <param argument="--samFlagInclude" type="integer" optional="True" value="" |
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189 label="Include reads based on the SAM flag" |
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190 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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191 <param argument="--samFlagExclude" type="integer" optional="True" value="" |
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192 label="Exclude reads based on the SAM flag" |
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193 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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194 </xml> |
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195 |
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196 <xml name="fragLength"> |
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197 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0" |
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198 label="Minimum fragment length for inclusion." |
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199 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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200 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0" |
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201 label="Maximum fragment length for inclusion." |
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202 help="A value of 0 (the default) is equivalent to no maximum." /> |
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203 </xml> |
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204 |
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205 <xml name="read_processing_options"> |
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206 <expand macro="extendReads" /> |
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207 <expand macro="ignoreDuplicates" /> |
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208 <expand macro="centerReads" /> |
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209 <expand macro="minMappingQuality" /> |
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210 <expand macro="samFlags" /> |
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211 <expand macro="fragLength" /> |
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212 </xml> |
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213 |
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214 <xml name="gtf_options"> |
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215 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue="" |
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216 label="Use a metagene model" |
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217 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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218 <param argument="--transcriptID" optional="True" value="transcript" type="text" |
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219 label="transcript designator" |
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220 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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221 <param argument="--exonID" optional="True" value="exon" type="text" |
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222 label="exon designator" |
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223 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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224 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" |
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225 label="transcriptID key designator" |
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226 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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227 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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228 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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229 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" /> |
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230 </xml> |
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231 |
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232 |
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233 <xml name="plotNumbers"> |
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234 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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235 label="Plot the correlation value" |
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236 help="If set, then the correlation number is plotted on top of the heatmap."/> |
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237 </xml> |
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238 |
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239 <xml name="extendReads"> |
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240 <conditional name="doExtendCustom"> |
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241 <param name="doExtend" type="select" label="Extend reads to the given average fragment size." |
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242 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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243 By default *each* read mate is extended. |
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244 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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245 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. |
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246 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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247 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> |
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248 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> |
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249 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> |
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250 <option value="custom">A custom length, which will be applied to ALL reads.</option> |
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251 </param> |
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252 <when value="no" /> |
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253 <when value="yes" /> |
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254 <when value="custom"> |
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255 <param name="extendReadsValue" type="integer" value="300" min="1" |
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256 label="Extend reads to the given average fragment size" |
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257 help="Extend all reads to this length" /> |
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258 </when> |
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259 </conditional> |
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260 </xml> |
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261 |
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262 <xml name="corMethod"> |
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263 <param argument="--corMethod" type="select" label="Correlation method"> |
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264 <option value="spearman" selected="True">Spearman</option> |
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265 <option value="pearson">Pearson</option> |
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266 </param> |
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267 </xml> |
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268 |
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269 <xml name="distanceBetweenBins"> |
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270 <param argument="--distanceBetweenBins" type="integer" value="0" min="0" |
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271 label="Distance between bins" |
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272 help="By default, multiBamSummary considers consecutive bins of |
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273 the specified 'Bin size'. However, to reduce the |
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274 computation time, a larger distance between bins can |
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275 be given. Larger distances result in fewer bins being |
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276 considered."/> |
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277 </xml> |
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278 |
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279 <xml name="centerReads"> |
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280 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" |
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281 label="Center regions with respect to the fragment length" |
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282 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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283 </xml> |
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284 |
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285 <xml name="ignoreDuplicates"> |
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286 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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287 label="Ignore duplicates" |
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288 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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289 </xml> |
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290 |
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291 <xml name="sortUsing"> |
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292 <param argument="--sortUsing" type="select" label="Method used for sorting" |
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293 help="For each row the method is computed."> |
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294 <option value="mean" selected="true">mean</option> |
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295 <option value="median">median</option> |
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296 <option value="min">min</option> |
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297 <option value="max">max</option> |
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298 <option value="sum">sum</option> |
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299 <option value="region_length">region length</option> |
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300 </param> |
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301 </xml> |
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302 |
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303 <xml name="sortRegionsComputeMatrix"> |
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304 <param argument="--sortRegions" type="select" label="Sort regions" |
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305 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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306 <option value="no">no ordering</option> |
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307 <option value="keep" selected="true">maintain the same ordering as the input files</option> |
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308 <option value="descend">descending order</option> |
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309 <option value="ascend">ascending order</option> |
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310 </param> |
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311 </xml> |
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312 |
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313 <xml name="sortRegions"> |
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314 <param argument="--sortRegions" type="select" label="Sort regions" |
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315 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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316 <option value="no">maintain the same ordering as the input files</option> |
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317 <option value="descend" selected="true">descending order</option> |
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318 <option value="ascend">ascending order</option> |
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319 </param> |
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320 </xml> |
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321 |
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322 <xml name="minMappingQuality"> |
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323 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0" |
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324 label="Minimum mapping quality" |
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325 help= "If set, only reads with a mapping quality score at least this high are considered."/> |
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326 </xml> |
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327 |
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328 <xml name="skipZeros"> |
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329 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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330 label ="Skip zeros" |
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331 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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332 </xml> |
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333 |
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334 <xml name="fragmentLength"> |
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335 <param argument="--fragmentLength" type="integer" min="1" optional="true" |
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336 label="Fragment length used for the sequencing" |
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337 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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338 </xml> |
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339 |
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340 <xml name="scaleFactor"> |
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341 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" |
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342 help="The computed scaling factor will be multiplied by this (default 1)." /> |
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343 </xml> |
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344 |
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345 <xml name="scaleFactors"> |
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346 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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347 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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348 </xml> |
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349 |
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350 <xml name="stdio"> |
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351 <stdio> |
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352 <exit_code range="1:" /> |
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353 <exit_code range=":-1" /> |
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354 <regex match="Error:" /> |
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355 <regex match="Exception:" /> |
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356 <regex match="EXception:" /> |
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357 <regex match="Traceback" /> |
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358 </stdio> |
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359 </xml> |
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360 |
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361 <xml name="pseudocount"> |
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362 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/> |
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363 </xml> |
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364 |
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365 <token name="@REFERENCES@"> |
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366 |
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367 .. class:: infomark |
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368 |
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369 For more information on the tools, please visit our `help site`_. |
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370 |
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371 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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372 |
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373 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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374 |
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375 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac |
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376 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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377 .. _help site: https://deeptools.readthedocs.org/ |
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378 |
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379 </token> |
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380 <xml name="citations"> |
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381 <citations> |
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382 <citation type="doi">10.1093/nar/gkw257</citation> |
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383 <yield /> |
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384 </citations> |
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385 </xml> |
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386 |
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387 <xml name="multiple_input_bams" tokens="MIN"> |
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388 <conditional name="multibam_conditional"> |
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389 <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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390 <option value="No" selected="true">No</option> |
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391 <option value="Yes">Yes</option> |
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392 </param> |
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393 <when value="No"> |
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394 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@" |
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395 label="BAM/CRAM file" multiple="true" |
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396 help=""/> |
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397 </when> |
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398 <when value="Yes"> |
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399 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files"> |
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400 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" /> |
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401 </repeat> |
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402 </when> |
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403 </conditional> |
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404 </xml> |
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405 |
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406 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE"> |
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407 <conditional name="multibigwig_conditional"> |
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408 <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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409 is vital to you, select Yes below."> |
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410 <option value="No" selected="true">No</option> |
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411 <option value="Yes">Yes</option> |
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412 </param> |
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413 <when value="No"> |
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414 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@" |
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415 label="@LABEL@" |
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416 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/> |
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417 </when> |
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418 <when value="Yes"> |
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419 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@"> |
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420 <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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421 </repeat> |
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422 </when> |
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423 </conditional> |
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424 </xml> |
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425 |
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426 <xml name="custom_sample_labels"> |
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427 <conditional name="custom_sample_labels_conditional"> |
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428 <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used."> |
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429 <option value="No" selected="true">No, use sample names in the history</option> |
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430 <option value="Yes">Yes, I want to specify new labels</option> |
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431 </param> |
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432 <when value="No"> |
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433 </when> |
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434 <when value="Yes"> |
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435 <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., "sample 1" "sample 2")"> |
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436 <sanitizer> |
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437 <valid initial="string.printable"> |
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438 </valid> |
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439 </sanitizer> |
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440 </param> |
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441 </when> |
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442 </conditional> |
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443 </xml> |
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444 |
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445 <xml name="plotTitle"> |
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446 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
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447 label="Title of the plot" |
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448 help="Title of the plot, to be printed on top of the generated image." /> |
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449 </xml> |
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450 |
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451 <xml name="legendLocation"> |
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452 <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile."> |
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453 <option value="best" selected="true">Best (automatic)</option> |
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454 <option value="upper-right">upper-right</option> |
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455 <option value="upper-left">upper-left</option> |
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456 <option value="upper-center">upper-center</option> |
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457 <option value="lower-right">lower-right</option> |
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458 <option value="lower-left">lower-left</option> |
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459 <option value="lower-center">lower-center</option> |
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460 <option value="center-right">center-right</option> |
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461 <option value="center-left">center-left</option> |
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462 <option value="center">center</option> |
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463 <option value="none">none (only works for heatmaps</option> |
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464 </param> |
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465 </xml> |
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466 |
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467 <xml name="labelRotation"> |
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468 <param argument="--labelRotation" type="integer" value="0" |
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469 label="Rotation of the X-axis labels (in degrees)" |
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470 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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471 </xml> |
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472 |
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473 |
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474 <token name="@multiple_input_bams@"> |
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475 <![CDATA[ |
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476 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": |
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477 #set custom_labels=labels |
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478 #end if |
0
49a569aecb22
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479 #set files=[] |
49a569aecb22
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480 #set labels=[] |
12
efc677b291c5
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481 #import re |
10
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482 #if $multibam_conditional.orderMatters == "No": |
163f2951146c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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483 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): |
12
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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484 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) |
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485 ln -s '${bamfile}' './${counter}.bam' && |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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486 #if $bamfile.ext == 'bam': |
78e60b236515
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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487 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && |
78e60b236515
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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488 #else: |
78e60b236515
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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489 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && |
78e60b236515
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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490 #end if |
78e60b236515
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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491 #silent $files.append("'%s.bam'" % $counter) |
12
efc677b291c5
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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492 #silent $labels.append("'%s'" % identifier) |
10
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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493 #end for |
163f2951146c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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494 #else: |
163f2951146c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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495 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): |
12
efc677b291c5
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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496 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) |
19
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497 ln -s '${f.bamfiles}' './${counter}.bam' && |
17
78e60b236515
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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498 #if $f.bamfiles.ext == 'bam': |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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499 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' && |
78e60b236515
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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500 #else: |
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501 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' && |
78e60b236515
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502 #end if |
78e60b236515
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503 #silent $files.append("'%s.bam'" % $counter) |
12
efc677b291c5
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504 #silent $labels.append("'%s'" % $identifier) |
10
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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505 #end for |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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506 #end if |
22
6f1cf6c1474b
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507 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": |
6f1cf6c1474b
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508 #set labels=custom_labels |
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509 #end if |
0
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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510 ]]> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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511 </token> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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512 |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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513 <token name="@multiple_input_bigwigs@"> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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514 <![CDATA[ |
22
6f1cf6c1474b
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515 #if $custom_labels_conditional.custom_labels_select == "Yes": |
6f1cf6c1474b
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516 #set custom_labels=labels |
6f1cf6c1474b
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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517 #end if |
0
49a569aecb22
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518 #set files=[] |
49a569aecb22
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519 #set labels=[] |
12
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520 #import re |
10
163f2951146c
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521 #if $multibigwig_conditional.orderMatters == "No": |
163f2951146c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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522 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): |
14
3b82b38fbaf3
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523 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) |
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524 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' && |
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525 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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526 #silent $labels.append("'%s'" % $identifier) |
10
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527 #end for |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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528 #else: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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529 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): |
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530 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) |
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531 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' && |
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532 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) |
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533 #silent $labels.append("'%s'" % $identifier) |
10
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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534 #end for |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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535 #end if |
22
6f1cf6c1474b
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536 #if $custom_labels_conditional.custom_labels_select == "Yes": |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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537 #set labels=custom_labels |
6f1cf6c1474b
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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538 #end if |
0
49a569aecb22
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539 ]]> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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540 </token> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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541 |
8
aec7ca832043
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542 <xml name="blacklist"> |
aec7ca832043
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543 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0" |
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544 label="Blacklisted regions in BED/GTF format" |
aec7ca832043
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545 help="One or more files containing regions to exclude from the analysis" /> |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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546 </xml> |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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547 |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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548 <token name="@blacklist@"> |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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549 <![CDATA[ |
aec7ca832043
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550 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None': |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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551 #set blfiles=[] |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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552 #for $f in $advancedOpt.blackListFileName: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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553 #silent $blfiles.append("'%s'" % $f) |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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554 #end for |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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555 #if $blfiles != ["'None'"]: |
aec7ca832043
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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556 --blackListFileName #echo ' '.join($blfiles)# |
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557 #end if |
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558 #end if |
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559 ]]> |
8
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560 </token> |
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561 |
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562 <xml name="multiple_bed"> |
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563 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true" |
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564 label="Regions in BED/GTF format" |
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565 help="One or more files containing regions to include in the analysis" /> |
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566 </xml> |
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567 |
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568 <token name="@multiple_bed@"> |
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569 <![CDATA[ |
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570 #set files=[] |
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571 #set labels=[] |
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572 #for $f in $BED: |
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573 #silent $files.append("'%s'" % $f) |
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574 #silent $labels.append("'%s'" % $f.display_name) |
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575 #end for |
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576 #if len($files) > 0: |
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577 --BED #echo ' '.join($files)# |
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578 --regionLabels #echo ' '.join($labels)# |
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579 #end if |
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580 ]]> |
8
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581 </token> |
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582 |
0
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583 <xml name="reference_genome_source"> |
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584 <conditional name="source"> |
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585 <param name="ref_source" type="select" label="Reference genome"> |
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586 <option value="cached">locally cached</option> |
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587 <option value="history">in your history</option> |
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588 </param> |
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589 <when value="cached"> |
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590 <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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591 <options from_data_table="lastz_seqs"> |
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592 <filter type="sort_by" column="1" /> |
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593 <validator type="no_options" message="No indexes are available." /> |
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594 </options> |
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595 </param> |
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596 </when> |
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597 <when value="history"> |
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598 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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599 </when> |
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600 </conditional> |
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601 </xml> |
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602 |
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603 <token name="@reference_genome_source@"> |
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604 #if $source.ref_source=="history": |
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605 --genome $source.input1 |
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606 #else: |
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607 --genome '$source.input1_2bit.fields.path' |
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608 #end if |
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609 </token> |
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610 |
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611 <xml name="effectiveGenomeSize"> |
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612 <conditional name="effectiveGenomeSize"> |
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613 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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614 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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615 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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616 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html"> |
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617 <option value="93260000">ce10 (93260000)</option> |
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618 <option value="130428560">dm3 (130428560)</option> |
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619 <option value="125464728">dm6 (125464728)</option> |
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620 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option> |
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621 <option value="2701495761">GRCh38/hg38 (2701495761)</option> |
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622 <option value="2304947926">GRCm37/mm9 (2304947926)</option> |
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623 <option value="2308125349">GRCm38/mm10 (2308125349)</option> |
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624 <option value="specific">user specified</option> |
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625 </param> |
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626 <when value="specific"> |
8
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627 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" |
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628 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/> |
0
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629 </when> |
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630 <when value="93260000" /> |
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631 <when value="130428560" /> |
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632 <when value="125464728" /> |
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633 <when value="2685511504" /> |
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634 <when value="2701495761" /> |
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635 <when value="2304947926" /> |
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636 <when value="2308125349" /> |
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637 </conditional> |
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638 </xml> |
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639 |
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640 <xml name="skipNAs"> |
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641 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" |
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642 label="Ignore missing data?" |
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643 help="This parameter determines if non-covered regions |
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644 (regions without overlapping reads) in a bam/bigWig file |
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645 should be skipped. The default is to treat those |
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646 regions as having a value of zero. The decision to |
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647 skip non-covered regions depends on the interpretation |
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648 of the data. Non-covered regions may represent, for |
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649 example, repetitive regions that should be ignored. |
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650 (default: False)" /> |
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651 </xml> |
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652 |
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653 <xml name="exactScaling"> |
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654 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False" |
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655 label="Compute an exact scaling factor" |
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656 help="Compute an exact scaling factor rather than one based on |
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657 sampled reads. This is only useful in cases where you are |
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658 filtering some alignments out AND this are both rare and |
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659 tend to clump together in the genome. In such cases the |
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660 region-based sampling employed by deepTools would produce |
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661 inaccurate scaling factors. Note that this option results |
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662 in the process taking significantly more time to complete." /> |
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663 </xml> |
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664 |
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665 <xml name="input_save_matrix_values"> |
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666 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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667 </xml> |
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668 |
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669 <xml name="input_graphic_output_settings"> |
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670 <conditional name="output" > |
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671 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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672 <option value="no" selected="true">no</option> |
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673 <option value="yes">yes</option> |
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674 </param> |
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675 <when value="no" /> |
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676 <when value="yes"> |
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677 <yield /> |
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678 <param name="saveSortedRegions" type="boolean" |
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679 argument="--outFileSortedRegions" |
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680 label="Save the regions after skipping zeros or min/max threshold values" |
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681 help="The order of the regions in the file follows the sorting order selected. This is useful, |
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682 for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
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683 </when> |
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684 </conditional> |
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685 </xml> |
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686 |
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687 |
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688 <xml name="input_image_file_format"> |
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689 <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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690 <option value="png" selected="true">png</option> |
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691 <option value="pdf">pdf</option> |
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692 <option value="svg">svg</option> |
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693 <option value="eps">eps</option> |
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694 <option value="plotly">plotly</option> |
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695 </param> |
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696 </xml> |
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697 |
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698 <xml name="output_dpi"> |
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699 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True" |
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700 label="Image dpi" help=""/> |
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701 </xml> |
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702 |
0
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703 <xml name="output_image_file_format"> |
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704 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image"> |
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705 <change_format> |
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706 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
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707 <when input="output.outFileFormat" value="svg" format="svg" /> |
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708 <when input="output.outFileFormat" value="eps" format="eps" /> |
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709 <when input="output.outFileFormat" value="plotly" format="html" /> |
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710 </change_format> |
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711 </data> |
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712 </xml> |
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713 |
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714 <xml name="output_image_file_format_not_nested"> |
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715 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image"> |
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|
716 <change_format> |
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717 <when input="outFileFormat" value="pdf" format="pdf" /> |
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718 <when input="outFileFormat" value="svg" format="svg" /> |
49a569aecb22
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719 <when input="outFileFormat" value="eps" format="eps" /> |
17
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|
720 <when input="outFileFormat" value="plotly" format="html" /> |
0
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|
721 </change_format> |
49a569aecb22
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722 </data> |
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|
723 </xml> |
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|
724 |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
725 <xml name="output_save_matrix_values"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
726 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
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|
727 <filter> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
728 (( |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
729 output['showOutputSettings'] == 'yes' and |
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|
730 output['saveMatrix'] is True |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
731 )) |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
732 </filter> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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733 </data> |
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|
734 </xml> |
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735 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
736 <xml name="output_graphic_outputs"> |
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|
737 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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738 <filter> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
739 (( |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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740 output['showOutputSettings'] == 'yes' and |
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|
741 output['saveSortedRegions'] is True |
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742 )) |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
743 </filter> |
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|
744 </data> |
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745 </xml> |
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|
746 |
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|
747 <xml name="colorMap"> |
8
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|
748 <param name="colorMap" type="select" label="Color map to use for the heatmap" |
17
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749 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"> |
0
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|
750 <option value="RdYlBu" selected="true">RdYlBu</option> |
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|
751 <option value="Accent">Accent</option> |
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|
752 <option value="Spectral">Spectral</option> |
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|
753 <option value="Set1">Set1</option> |
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754 <option value="Set2">Set2</option> |
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|
755 <option value="Set3">Set3</option> |
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|
756 <option value="Dark2">Dark2</option> |
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|
757 <option value="Reds">Reds</option> |
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|
758 <option value="Oranges">Oranges</option> |
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changeset
|
759 <option value="Greens">Greens</option> |
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|
760 <option value="Blues">Blues</option> |
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|
761 <option value="Greys">Greys</option> |
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|
762 <option value="Purples">Purples</option> |
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|
763 <option value="Paired">Paired</option> |
49a569aecb22
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|
764 <option value="Pastel1">Pastel1</option> |
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|
765 <option value="Pastel2">Pastel2</option> |
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|
766 <option value="spring">spring</option> |
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|
767 <option value="summer">summer</option> |
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|
768 <option value="autumn">autumn</option> |
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|
769 <option value="winter">winter</option> |
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|
770 <option value="hot">hot</option> |
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|
771 <option value="coolwarm">coolwarm</option> |
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|
772 <option value="cool">cool</option> |
49a569aecb22
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|
773 <option value="seismic">seismic</option> |
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|
774 <option value="terrain">terrain</option> |
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|
775 <option value="ocean">ocean</option> |
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|
776 <option value="rainbow">rainbow</option> |
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|
777 <option value="bone">bone</option> |
49a569aecb22
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|
778 <option value="flag">flag</option> |
49a569aecb22
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|
779 <option value="prism">prism</option> |
49a569aecb22
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|
780 <option value="cubehelix">cubehelix</option> |
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|
781 <option value="binary">binary</option> |
49a569aecb22
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|
782 <option value="pink">pink</option> |
49a569aecb22
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|
783 <option value="gray">gray</option> |
49a569aecb22
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|
784 <option value="copper">copper</option> |
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|
785 <option value="BrBG">BrBG</option> |
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|
786 <option value="BuGn">BuGn</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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changeset
|
787 <option value="BuPu">BuPu</option> |
49a569aecb22
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changeset
|
788 <option value="GnBu">GnBu</option> |
49a569aecb22
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|
789 <option value="OrRd">OrRd</option> |
49a569aecb22
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|
790 <option value="PiYG">PiYG</option> |
49a569aecb22
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|
791 <option value="PRGn">PRGn</option> |
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|
792 <option value="PuOr">PuOr</option> |
49a569aecb22
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|
793 <option value="PuRd">PuRd</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
794 <option value="PuBu">PuBu</option> |
49a569aecb22
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changeset
|
795 <option value="RdBu">RdBu</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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|
796 <option value="RdGy">RdGy</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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diff
changeset
|
797 <option value="RdPu">RdPu</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
798 <option value="YlGn">YlGn</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
799 <option value="PuBuGn">PuBuGn</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
800 <option value="RdYlGn">RdYlGn</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
801 <option value="YlGnBu">YlGnBu</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
802 <option value="YlOrBr">YlOrBr</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
803 <option value="YlOrRd">YlOrRd</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
804 <option value="gist_gray">gist_gray</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
805 <option value="gist_stern">gist_stern</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
806 <option value="gist_earth">gist_earth</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
807 <option value="gist_yarg">gist_yarg</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
808 <option value="gist_ncar">gist_ncar</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
809 <option value="gist_rainbow">gist_rainbow</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
810 <option value="gist_heat">gist_heat</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
811 <option value="gnuplot">gnuplot</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
812 <option value="gnuplot2">gnuplot2</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
813 <option value="CMRmap">CMRmap</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
814 <option value="bwr">bwr</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
815 <option value="hsv">hsv</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
816 <option value="brg">brg</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
817 <option value="jet">jet</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
818 <option value="afmhot">afmhot</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
819 <option value="Accent_r">Accent reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
820 <option value="Spectral_r">Spectral reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
821 <option value="Set1_r">Set1 reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
822 <option value="Set2_r">Set2 reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
823 <option value="Set3_r">Set3 reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
824 <option value="Dark2_r">Dark2 reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
825 <option value="Reds_r">Reds reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
826 <option value="Oranges_r">Oranges reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
827 <option value="Greens_r">Greens reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
828 <option value="Blues_r">Blues reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
829 <option value="Greys_r">Greys reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
830 <option value="Purples_r">Purples reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
831 <option value="Paired_r">Paired reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
832 <option value="Pastel1_r">Pastel1 reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
833 <option value="Pastel2_r">Pastel2 reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
834 <option value="spring_r">spring reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
835 <option value="summer_r">summer reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
836 <option value="autumn_r">autumn reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
837 <option value="winter_r">winter reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
838 <option value="hot_r">hot reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
839 <option value="coolwarm_r">coolwarm reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
840 <option value="cool_r">cool reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
841 <option value="seismic_r">seismic reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
842 <option value="terrain_r">terrain reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
843 <option value="ocean_r">ocean reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
844 <option value="rainbow_r">rainbow reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
845 <option value="bone_r">bone reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
846 <option value="flag_r">flag reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
847 <option value="prism_r">prism reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
848 <option value="cubehelix_r">cubehelix reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
849 <option value="binary_r">binary reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
850 <option value="pink_r">pink reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
851 <option value="gray_r">gray reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
852 <option value="copper_r">copper reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
853 <option value="BrBG_r">BrBG reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
854 <option value="BuGn_r">BuGn reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
855 <option value="BuPu_r">BuPu reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
856 <option value="GnBu_r">GnBu reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
857 <option value="OrRd_r">OrRd reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
858 <option value="PiYG_r">PiYG reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
859 <option value="PRGn_r">PRGn reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
860 <option value="PuOr_r">PuOr reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
861 <option value="PuRd_r">PuRd reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
862 <option value="PuBu_r">PuBu reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
863 <option value="RdBu_r">RdBu reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
864 <option value="RdGy_r">RdGy reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
865 <option value="RdPu_r">RdPu reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
866 <option value="YlGn_r">YlGn reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
867 <option value="PuBuGn_r">PuBuGn reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
868 <option value="RdYlBu_r">RdYlBu reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
869 <option value="RdYlGn_r">RdYlGn reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
870 <option value="YlGnBu_r">YlGnBu reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
871 <option value="YlOrBr_r">YlOrBr reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
872 <option value="YlOrRd_r">YlOrRd reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
873 <option value="gist_gray_r">gist_gray reversed</option> |
49a569aecb22
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874 <option value="gist_stern_r">gist_stern reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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875 <option value="gist_earth_r">gist_earth reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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876 <option value="gist_yarg_r">gist_yarg reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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877 <option value="gist_ncar_r">gist_ncar reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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878 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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879 <option value="gist_heat_r">gist_heat reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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880 <option value="gnuplot_r">gnuplot reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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881 <option value="gnuplot2_r">gnuplot2 reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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882 <option value="CMRmap_r">CMRmap reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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883 <option value="bwr_r">bwr reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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884 <option value="hsv_r">hsv reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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885 <option value="brg_r">brg reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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886 <option value="jet_r">jet reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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887 <option value="afmhot_r">afmhot reversed</option> |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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888 </param> |
49a569aecb22
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889 |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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890 </xml> |
49a569aecb22
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891 |
49a569aecb22
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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892 </macros> |