Mercurial > repos > bgruening > deeptools_bam_compare
annotate deepTools_macros.xml @ 8:89f6d2283317 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
author | bgruening |
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date | Tue, 20 Sep 2016 03:06:21 -0400 |
parents | d5d57b40b29a |
children | 6aee99aec0d1 |
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105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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1 <macros> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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2 |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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3 <xml name="advancedOpt_scaffold"> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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4 <conditional name="advancedOpt"> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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5 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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6 <option value="no" selected="true">no</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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7 <option value="yes">yes</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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8 </param> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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9 <when value="no" /> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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10 <when value="yes"> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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11 <yield/> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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12 </when> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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13 </conditional> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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14 </xml> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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15 |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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16 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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17 #if $advancedOpt.doExtendCustom.doExtend == 'custom': |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes': |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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20 --extendReads |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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21 #end if |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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22 $advancedOpt.ignoreDuplicates |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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23 $advancedOpt.centerReads |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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24 #if $advancedOpt.minMappingQuality: |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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25 --minMappingQuality '$advancedOpt.minMappingQuality' |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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26 #end if |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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27 #if $advancedOpt.samFlagInclude: |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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28 --samFlagInclude $advancedOpt.samFlagInclude |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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29 #end if |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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30 #if $advancedOpt.samFlagExclude: |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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31 --samFlagExclude $advancedOpt.samFlagExclude |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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32 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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33 #if $advancedOpt.minFragmentLength: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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34 --minFragmentLength $advancedOpt.minFragmentLength |
89f6d2283317
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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35 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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36 #if $advancedOpt.maxFragmentLength: |
89f6d2283317
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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37 --maxFragmentLength $advancedOpt.maxFragmentLength |
89f6d2283317
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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38 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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39 </token> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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40 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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41 <token name="@ADVANCED_OPTS_GTF@"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
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42 $advancedOpt.metagene |
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43 #if $advancedOpt.transcriptID: |
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44 --transcriptID $advancedOpt.transcriptID |
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45 #end if |
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46 #if $advancedOpt.exonID: |
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47 --exonID $advancedOpt.exonID |
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48 #end if |
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49 #if $advancedOpt.transcript_id_designator: |
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50 --transcript_id_designator $advancedOpt.transcript_id_designator |
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51 #end if |
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52 </token> |
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53 |
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54 <xml name="heatmap_options"> |
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55 <expand macro="zMin_zMax" /> |
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56 <expand macro="colorMap" /> |
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57 <expand macro="plotTitle" /> |
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58 <expand macro="plotNumbers" /> |
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59 </xml> |
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60 |
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61 <token name="@HEATMAP_OPTIONS@"> |
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62 #if str($plotting_type.zMin) != "": |
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63 --zMin $plotting_type.zMin |
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64 #end if |
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65 #if str($plotting_type.zMax) != "": |
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66 --zMax $plotting_type.zMax |
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67 #end if |
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68 --colorMap '$plotting_type.colorMap' |
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69 $plotting_type.plotNumbers |
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70 --plotTitle '$plotting_type.plotTitle' |
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71 </token> |
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72 |
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73 |
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74 <xml name="includeZeros"> |
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75 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
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76 label="Include zeros" |
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77 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." /> |
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78 </xml> |
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79 |
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80 <xml name="zMin_zMax"> |
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81 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities" |
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82 help="If not specified the value is set automatically."/> |
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83 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities" |
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84 help="If not specified the value is set automatically."/> |
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85 </xml> |
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86 |
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87 <xml name="region_limit_operation"> |
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88 <param argument="--region" type="text" value="" |
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89 label="Region of the genome to limit the operation to" |
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90 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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91 <sanitizer> |
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92 <valid initial="string.letters,string.digits"> |
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93 <add value="|"/> |
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94 <add value=":"/> |
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95 </valid> |
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96 </sanitizer> |
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97 </param> |
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98 </xml> |
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99 |
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100 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
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101 <token name="@WRAPPER_VERSION@">2.3.5</token> |
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102 <xml name="requirements"> |
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103 <requirements> |
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104 <requirement type="package" version="2.7.10">python</requirement> |
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105 <requirement type="package" version="2.3.5">deepTools</requirement> |
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106 <yield /> |
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107 </requirements> |
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108 <expand macro="stdio" /> |
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109 <version_command>@BINARY@ --version</version_command> |
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110 </xml> |
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111 |
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112 <xml name="smoothLength"> |
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113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1" |
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114 label="Smooth values using the following length (in bases)" |
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115 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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116 </xml> |
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117 |
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118 |
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119 <xml name="kmeans_clustering"> |
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120 <conditional name="used_multiple_regions"> |
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121 <param name="used_multiple_regions_options" type="select" |
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122 label="Did you compute the matrix with more than one groups of regions?" |
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123 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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124 <option value="yes">Yes, I used multiple groups of regions</option> |
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125 <option value="no">No, I used only one group</option> |
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126 </param> |
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127 <when value="no"> |
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128 <conditional name="clustering"> |
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129 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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130 <option value="none">No clustering</option> |
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131 <option value="kmeans">Kmeans clustering</option> |
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132 <option value="hclust">Hierarchical clustering</option> |
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133 </param> |
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134 <when value="kmeans"> |
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135 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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136 help="When this option is set, the matrix is split into clusters using the k-means algorithm. |
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137 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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138 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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139 run the clustering using other software."/> |
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140 </when> |
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141 <when value="hclust"> |
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142 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." |
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143 help="WARNING: This option causes the tool to run for a very long time! When this option is |
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144 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. |
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145 This only works for data that is not grouped, otherwise only the first group will be clustered. |
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146 Note that you must have used the '--missingDataAsZero' option within computeMatrix! |
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147 If more specific clustering methods are required it is advisable to save the underlying matrix and |
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148 run the clustering using other software."/> |
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149 </when> |
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150 <when value="none" /> |
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151 </conditional> |
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152 </when> |
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153 <when value="yes" /> |
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154 </conditional> |
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155 </xml> |
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156 |
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157 <token name="@KMEANS_CLUSTERING@"> |
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158 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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159 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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160 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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161 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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162 #end if |
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163 #end if |
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164 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': |
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165 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: |
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166 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust |
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167 #end if |
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168 #end if |
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169 #end if |
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170 </token> |
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171 |
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172 <xml name="samFlags"> |
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173 <param argument="--samFlagInclude" type="integer" optional="True" value="" |
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174 label="Include reads based on the SAM flag" |
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175 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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176 <param argument="--samFlagExclude" type="integer" optional="True" value="" |
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177 label="Exclude reads based on the SAM flag" |
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178 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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179 </xml> |
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180 |
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181 <xml name="fragLength"> |
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182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0" |
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183 label="Minimum fragment length for inclusion." |
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184 help="A value greater than 0 will filter out ALL single-end reads. 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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185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0" |
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186 label="Maximum fragment length for inclusion." |
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187 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." /> |
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188 </xml> |
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189 |
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190 <xml name="read_processing_options"> |
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191 <expand macro="extendReads" /> |
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192 <expand macro="ignoreDuplicates" /> |
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193 <expand macro="centerReads" /> |
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194 <expand macro="minMappingQuality" /> |
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195 <expand macro="samFlags" /> |
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196 <expand macro="fragLength" /> |
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197 </xml> |
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198 |
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199 <xml name="gtf_options"> |
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200 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue="" |
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201 label="Use a metagene model" |
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202 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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203 <param argument="--transcriptID" optional="True" value="transcript" type="text" |
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204 label="trascript designator" |
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205 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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206 <param argument="--exonID" optional="True" value="exon" type="text" |
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207 label="exon designator" |
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208 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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209 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" |
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210 label="transcriptID key designator" |
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211 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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212 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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213 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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214 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" /> |
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215 </xml> |
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216 |
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217 |
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218 <xml name="plotNumbers"> |
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219 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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220 label="Plot the correlation value" |
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221 help="If set, then the correlation number is plotted on top of the heatmap."/> |
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222 </xml> |
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223 |
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224 <xml name="extendReads"> |
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225 <conditional name="doExtendCustom"> |
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226 <param name="doExtend" type="select" label="Extend reads to the given average fragment size." |
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227 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here. |
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228 By default *each* read mate is extended. |
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229 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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230 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. |
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231 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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232 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> |
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233 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> |
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234 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> |
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235 <option value="custom">A custom length, which will be applied to ALL reads.</option> |
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236 </param> |
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237 <when value="no" /> |
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238 <when value="yes" /> |
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239 <when value="custom"> |
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240 <param name="extendReadsValue" type="integer" value="300" min="1" |
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241 label="Extend reads to the given average fragment size" |
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242 help="Extend all reads to this length" /> |
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243 </when> |
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244 </conditional> |
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245 </xml> |
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246 |
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247 <xml name="corMethod"> |
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248 <param argument="--corMethod" type="select" label="Correlation method"> |
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249 <option value="spearman" selected="True">Spearman</option> |
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250 <option value="pearson">Pearson</option> |
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251 </param> |
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252 </xml> |
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253 |
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254 <xml name="distanceBetweenBins"> |
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255 <param argument="--distanceBetweenBins" type="integer" value="0" min="0" |
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256 label="Distance between bins" |
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257 help="By default, multiBamSummary considers consecutive bins of |
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258 the specified 'Bin size'. However, to reduce the |
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259 computation time, a larger distance between bins can |
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260 be given. Larger distances result in fewer bins being |
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261 considered."/> |
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262 </xml> |
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263 |
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264 <xml name="centerReads"> |
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265 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" |
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266 label="Center regions with respect to the fragment length" |
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267 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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268 </xml> |
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269 |
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270 <xml name="ignoreDuplicates"> |
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271 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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272 label="Ignore duplicates" |
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273 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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274 </xml> |
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275 |
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276 <xml name="sortUsing"> |
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277 <param argument="--sortUsing" type="select" label="Method used for sorting" |
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278 help="For each row the method is computed."> |
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279 <option value="mean" selected="true">mean</option> |
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280 <option value="median">median</option> |
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281 <option value="min">min</option> |
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282 <option value="max">max</option> |
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283 <option value="sum">sum</option> |
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284 <option value="region_length">region length</option> |
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285 </param> |
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286 </xml> |
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287 |
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288 <xml name="sortRegions"> |
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289 <param argument="--sortRegions" type="select" label="Sort regions" |
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290 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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291 <option value="no">no ordering</option> |
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292 <option value="descend" selected="true">descending order</option> |
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293 <option value="ascend">ascending order</option> |
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294 </param> |
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295 </xml> |
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296 |
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297 <xml name="minMappingQuality"> |
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298 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0" |
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299 label="Minimum mapping quality" |
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300 help= "If set, only reads with a mapping quality score higher than this value are considered."/> |
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301 </xml> |
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302 |
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303 <xml name="skipZeros"> |
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304 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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305 label ="Skip zeros" |
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306 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." /> |
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307 </xml> |
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308 |
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309 <xml name="fragmentLength"> |
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310 <param argument="--fragmentLength" type="integer" value="300" min="1" |
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311 label="Fragment length used for the sequencing" |
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312 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/> |
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313 </xml> |
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314 |
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315 <xml name="scaleFactor"> |
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316 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" |
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317 help="When used in combination with --normalizeTo1x or |
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318 --normalizeUsingRPKM, the computed scaling factor will |
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319 be multiplied by the given scale factor." /> |
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320 </xml> |
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321 |
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322 <xml name="scaleFactors"> |
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323 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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324 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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325 </xml> |
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326 |
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327 <xml name="stdio"> |
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328 <stdio> |
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329 <exit_code range="1:" /> |
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330 <exit_code range=":-1" /> |
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331 <regex match="Error:" /> |
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332 <regex match="Exception:" /> |
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333 <regex match="EXception:" /> |
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334 <regex match="Traceback" /> |
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335 </stdio> |
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336 </xml> |
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337 |
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338 <xml name="pseudocount"> |
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339 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
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340 </xml> |
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341 |
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342 <token name="@REFERENCES@"> |
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343 |
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344 .. class:: infomark |
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345 |
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346 For more information on the tools, please visit our `help site`_. |
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347 |
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348 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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349 |
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350 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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351 |
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352 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac |
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353 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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354 .. _help site: https://deeptools.readthedocs.org/ |
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355 |
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356 </token> |
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357 <xml name="citations"> |
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358 <citations> |
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359 <citation type="doi">10.1093/nar/gkw257</citation> |
0
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360 <yield /> |
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361 </citations> |
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362 </xml> |
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363 |
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364 <xml name="multiple_input_bams"> |
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365 <param argument="--bamfiles" type="data" format="bam" min="1" |
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366 label="Bam file" multiple="true" |
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367 help=""/> |
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368 </xml> |
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369 |
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370 <xml name="multiple_input_bams_min2"> |
0
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371 <param argument="--bamfiles" type="data" format="bam" min="2" |
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372 label="Bam file" multiple="true" |
3
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373 help=""/> |
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374 </xml> |
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375 |
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376 <xml name="multiple_input_bigwigs"> |
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377 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" |
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378 label="Bigwig file" |
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379 help="A Bigwig file."/> |
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380 </xml> |
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381 |
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382 <xml name="plotTitle"> |
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383 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
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384 label="Title of the plot" |
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385 help="Title of the plot, to be printed on top of the generated image." /> |
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386 </xml> |
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387 |
1
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388 |
0
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389 <token name="@multiple_input_bams@"> |
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390 <![CDATA[ |
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391 #set files=[] |
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392 #set labels=[] |
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393 #for $counter, $bamfile in enumerate($bamfiles): |
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394 ln -s "${bamfile}" "./${counter}.bam" && |
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395 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && |
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396 #silent $files.append('%s.bam' % $counter) |
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397 #silent $labels.append("'%s'" % ($bamfile.display_name)) |
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398 #end for |
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399 ]]> |
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400 </token> |
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401 |
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402 <token name="@multiple_input_bigwigs@"> |
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403 <![CDATA[ |
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404 #set files=[] |
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405 #set labels=[] |
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406 #for $counter, $bigwig in enumerate($bigwigfiles): |
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407 ln -s "${bigwig}" "${counter}.bw" && |
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408 #silent $files.append('%s.bw' % $counter) |
5
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409 #silent $labels.append("'%s'" % ($bigwig.display_name)) |
0
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410 #end for |
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411 ]]> |
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412 </token> |
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413 |
8
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414 <xml name="blacklist"> |
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415 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0" |
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416 label="Blacklisted regions in BED/GTF format" |
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417 help="One or more files containing regions to exclude from the analysis" /> |
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418 </xml> |
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419 |
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420 <token name="@blacklist@"> |
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421 <![CDATA[ |
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422 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None': |
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423 #set blfiles=[] |
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424 #for $f in $advancedOpt.blackListFileName: |
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425 #silent $blfiles.append("'%s'" % $f) |
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426 #end for |
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427 #if $blfiles != ["'None'"]: |
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428 --blackListFileName #echo ' '.join($blfiles)# |
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429 #end if |
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430 #end if |
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431 ]]> |
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432 </token> |
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433 |
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434 <xml name="multiple_bed"> |
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435 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true" |
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436 label="Regions in BED/GTF format" |
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437 help="One or more files containing regions to include in the analysis" /> |
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438 </xml> |
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439 |
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440 <token name="@multiple_bed@"> |
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441 <![CDATA[ |
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442 #set files=[] |
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443 #set labels=[] |
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444 #for $f in $BED: |
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445 #silent $files.append("'%s'" % $f) |
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446 #silent $labels.append("'%s'" % $f.display_name) |
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447 #end for |
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448 #if len($files) > 0: |
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449 --BED #echo ' '.join($files)# |
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450 --regionLabels #echo ' '.join($labels)# |
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451 #end if |
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452 ]]> |
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453 </token> |
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454 |
0
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455 <xml name="reference_genome_source"> |
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456 <conditional name="source"> |
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457 <param name="ref_source" type="select" label="Reference genome"> |
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458 <option value="cached">locally cached</option> |
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459 <option value="history">in your history</option> |
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460 </param> |
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461 <when value="cached"> |
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462 <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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463 <options from_data_table="lastz_seqs"> |
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464 <filter type="sort_by" column="1" /> |
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465 <validator type="no_options" message="No indexes are available." /> |
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466 </options> |
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467 </param> |
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468 </when> |
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469 <when value="history"> |
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470 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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471 </when> |
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472 </conditional> |
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473 </xml> |
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474 |
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475 <token name="@reference_genome_source@"> |
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476 #if $source.ref_source=="history": |
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477 --genome $source.input1 |
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478 #else: |
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479 --genome "$source.input1_2bit.fields.path" |
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480 #end if |
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481 </token> |
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482 |
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483 <xml name="effectiveGenomeSize"> |
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484 <conditional name="effectiveGenomeSize"> |
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485 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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486 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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487 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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488 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> |
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489 <option value="93260000">ce10 (93260000)</option> |
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490 <option value="121400000">dm3 (121400000)</option> |
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491 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
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492 <option value="2150570000">mm9 (2150570000)</option> |
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493 <option value="specific">user specified</option> |
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494 </param> |
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495 <when value="specific"> |
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496 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" |
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497 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> |
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498 </when> |
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499 <when value="2150570000" /> |
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500 <when value="2451960000" /> |
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501 <when value="121400000" /> |
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502 <when value="93260000" /> |
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503 </conditional> |
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504 </xml> |
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505 |
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506 <xml name="skipNAs"> |
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507 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" |
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508 label="Ignore missing data?" |
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509 help="This parameter determines if non-covered regions |
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510 (regions without overlapping reads) in a bam/bigWig file |
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511 should be skipped. The default is to treat those |
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512 regions as having a value of zero. The decision to |
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513 skip non-covered regions depends on the interpretation |
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514 of the data. Non-covered regions may represent, for |
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515 example, repetitive regions that should be ignored. |
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516 (default: False)" /> |
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517 </xml> |
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518 |
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519 <xml name="input_save_matrix_values"> |
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520 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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521 </xml> |
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522 |
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523 <xml name="input_graphic_output_settings"> |
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524 <conditional name="output" > |
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525 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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526 <option value="no" selected="true">no</option> |
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527 <option value="yes">yes</option> |
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528 </param> |
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529 <when value="no" /> |
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530 <when value="yes"> |
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531 <yield /> |
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532 <param name="saveSortedRegions" type="boolean" |
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533 label="Save the regions after skipping zeros or min/max threshold values" |
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534 help="The order of the regions in the file follows the sorting order selected. This is useful, |
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535 for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
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536 </when> |
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537 </conditional> |
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538 </xml> |
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539 |
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540 |
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541 <xml name="input_image_file_format"> |
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542 <param argument="--outFileFormat" type="select" label="Image file format"> |
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543 <option value="png" selected="true">png</option> |
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544 <option value="pdf">pdf</option> |
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545 <option value="svg">svg</option> |
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546 <option value="eps">eps</option> |
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547 </param> |
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548 </xml> |
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549 |
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550 <xml name="output_dpi"> |
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551 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True" |
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552 label="Image dpi" help=""/> |
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553 </xml> |
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554 |
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555 <xml name="output_image_file_format"> |
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556 <data format="png" name="outFileName" label="${tool.name} image"> |
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557 <change_format> |
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558 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
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559 <when input="output.outFileFormat" value="svg" format="svg" /> |
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560 <when input="output.outFileFormat" value="eps" format="eps" /> |
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561 </change_format> |
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562 </data> |
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563 </xml> |
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564 |
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565 <xml name="output_image_file_format_not_nested"> |
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566 <data format="png" name="outFileName" label="${tool.name} image"> |
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567 <change_format> |
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568 <when input="outFileFormat" value="pdf" format="pdf" /> |
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569 <when input="outFileFormat" value="svg" format="svg" /> |
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570 <when input="outFileFormat" value="eps" format="eps" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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571 </change_format> |
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572 </data> |
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573 </xml> |
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574 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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575 <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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576 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
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577 <filter> |
105b9da2445c
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578 (( |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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579 output['showOutputSettings'] == 'yes' and |
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580 output['saveMatrix'] is True |
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581 )) |
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582 </filter> |
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583 </data> |
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584 </xml> |
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585 |
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586 <xml name="output_graphic_outputs"> |
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587 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
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588 <filter> |
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589 (( |
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590 output['showOutputSettings'] == 'yes' and |
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591 output['saveSortedRegions'] is True |
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592 )) |
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593 </filter> |
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594 </data> |
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595 </xml> |
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596 |
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597 <xml name="colorMap"> |
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598 <param name="colorMap" type="select" label="Color map to use for the heatmap" |
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599 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html" |
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600 multiple="true"> |
0
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601 <option value="RdYlBu" selected="true">RdYlBu</option> |
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602 <option value="Accent">Accent</option> |
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603 <option value="Spectral">Spectral</option> |
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604 <option value="Set1">Set1</option> |
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605 <option value="Set2">Set2</option> |
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606 <option value="Set3">Set3</option> |
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607 <option value="Dark2">Dark2</option> |
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608 <option value="Reds">Reds</option> |
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609 <option value="Oranges">Oranges</option> |
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610 <option value="Greens">Greens</option> |
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611 <option value="Blues">Blues</option> |
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612 <option value="Greys">Greys</option> |
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613 <option value="Purples">Purples</option> |
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614 <option value="Paired">Paired</option> |
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615 <option value="Pastel1">Pastel1</option> |
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616 <option value="Pastel2">Pastel2</option> |
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617 <option value="spring">spring</option> |
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618 <option value="summer">summer</option> |
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619 <option value="autumn">autumn</option> |
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620 <option value="winter">winter</option> |
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621 <option value="hot">hot</option> |
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622 <option value="coolwarm">coolwarm</option> |
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623 <option value="cool">cool</option> |
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624 <option value="seismic">seismic</option> |
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625 <option value="terrain">terrain</option> |
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626 <option value="ocean">ocean</option> |
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627 <option value="rainbow">rainbow</option> |
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628 <option value="bone">bone</option> |
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629 <option value="flag">flag</option> |
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630 <option value="prism">prism</option> |
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631 <option value="cubehelix">cubehelix</option> |
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632 <option value="binary">binary</option> |
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633 <option value="pink">pink</option> |
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634 <option value="gray">gray</option> |
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635 <option value="copper">copper</option> |
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636 <option value="BrBG">BrBG</option> |
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637 <option value="BuGn">BuGn</option> |
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638 <option value="BuPu">BuPu</option> |
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639 <option value="GnBu">GnBu</option> |
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640 <option value="OrRd">OrRd</option> |
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641 <option value="PiYG">PiYG</option> |
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642 <option value="PRGn">PRGn</option> |
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643 <option value="PuOr">PuOr</option> |
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644 <option value="PuRd">PuRd</option> |
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645 <option value="PuBu">PuBu</option> |
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646 <option value="RdBu">RdBu</option> |
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647 <option value="RdGy">RdGy</option> |
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648 <option value="RdPu">RdPu</option> |
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diff
changeset
|
649 <option value="YlGn">YlGn</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
650 <option value="PuBuGn">PuBuGn</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
651 <option value="RdYlGn">RdYlGn</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
652 <option value="YlGnBu">YlGnBu</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
653 <option value="YlOrBr">YlOrBr</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
654 <option value="YlOrRd">YlOrRd</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
655 <option value="gist_gray">gist_gray</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
656 <option value="gist_stern">gist_stern</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
657 <option value="gist_earth">gist_earth</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
658 <option value="gist_yarg">gist_yarg</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
659 <option value="gist_ncar">gist_ncar</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
660 <option value="gist_rainbow">gist_rainbow</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
661 <option value="gist_heat">gist_heat</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
662 <option value="gnuplot">gnuplot</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
663 <option value="gnuplot2">gnuplot2</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
664 <option value="CMRmap">CMRmap</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
665 <option value="bwr">bwr</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
666 <option value="hsv">hsv</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
667 <option value="brg">brg</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
668 <option value="jet">jet</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
669 <option value="afmhot">afmhot</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
670 <option value="Accent_r">Accent reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
671 <option value="Spectral_r">Spectral reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
672 <option value="Set1_r">Set1 reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
673 <option value="Set2_r">Set2 reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
674 <option value="Set3_r">Set3 reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
675 <option value="Dark2_r">Dark2 reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
676 <option value="Reds_r">Reds reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
677 <option value="Oranges_r">Oranges reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
678 <option value="Greens_r">Greens reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
679 <option value="Blues_r">Blues reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
680 <option value="Greys_r">Greys reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
681 <option value="Purples_r">Purples reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
682 <option value="Paired_r">Paired reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
683 <option value="Pastel1_r">Pastel1 reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
684 <option value="Pastel2_r">Pastel2 reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
685 <option value="spring_r">spring reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
686 <option value="summer_r">summer reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
687 <option value="autumn_r">autumn reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
688 <option value="winter_r">winter reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
689 <option value="hot_r">hot reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
690 <option value="coolwarm_r">coolwarm reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
691 <option value="cool_r">cool reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
692 <option value="seismic_r">seismic reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
693 <option value="terrain_r">terrain reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
694 <option value="ocean_r">ocean reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
695 <option value="rainbow_r">rainbow reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
696 <option value="bone_r">bone reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
697 <option value="flag_r">flag reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
698 <option value="prism_r">prism reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
699 <option value="cubehelix_r">cubehelix reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
700 <option value="binary_r">binary reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
701 <option value="pink_r">pink reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
702 <option value="gray_r">gray reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
703 <option value="copper_r">copper reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
704 <option value="BrBG_r">BrBG reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
705 <option value="BuGn_r">BuGn reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
706 <option value="BuPu_r">BuPu reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
707 <option value="GnBu_r">GnBu reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
708 <option value="OrRd_r">OrRd reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
709 <option value="PiYG_r">PiYG reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
710 <option value="PRGn_r">PRGn reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
711 <option value="PuOr_r">PuOr reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
712 <option value="PuRd_r">PuRd reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
713 <option value="PuBu_r">PuBu reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
714 <option value="RdBu_r">RdBu reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
715 <option value="RdGy_r">RdGy reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
716 <option value="RdPu_r">RdPu reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
717 <option value="YlGn_r">YlGn reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
718 <option value="PuBuGn_r">PuBuGn reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
719 <option value="RdYlBu_r">RdYlBu reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
720 <option value="RdYlGn_r">RdYlGn reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
721 <option value="YlGnBu_r">YlGnBu reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
722 <option value="YlOrBr_r">YlOrBr reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
723 <option value="YlOrRd_r">YlOrRd reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
724 <option value="gist_gray_r">gist_gray reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
725 <option value="gist_stern_r">gist_stern reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
726 <option value="gist_earth_r">gist_earth reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
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changeset
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727 <option value="gist_yarg_r">gist_yarg reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
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728 <option value="gist_ncar_r">gist_ncar reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
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changeset
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729 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
730 <option value="gist_heat_r">gist_heat reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
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changeset
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731 <option value="gnuplot_r">gnuplot reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
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diff
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732 <option value="gnuplot2_r">gnuplot2 reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
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733 <option value="CMRmap_r">CMRmap reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
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734 <option value="bwr_r">bwr reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
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735 <option value="hsv_r">hsv reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
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736 <option value="brg_r">brg reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
737 <option value="jet_r">jet reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
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diff
changeset
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738 <option value="afmhot_r">afmhot reversed</option> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
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diff
changeset
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739 </param> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
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740 |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
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changeset
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741 </xml> |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
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742 |
105b9da2445c
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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743 </macros> |