Mercurial > repos > bgruening > deeptools_plot_pca
annotate deepTools_macros.xml @ 1:439451971446 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
author | bgruening |
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date | Fri, 18 Dec 2015 08:01:12 -0500 |
parents | a6fdea25d41f |
children | 828ecc09ca38 |
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a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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1 <macros> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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2 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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3 <xml name="advancedOpt_scaffold"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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4 <conditional name="advancedOpt"> |
a6fdea25d41f
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5 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
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6 <option value="no" selected="true">no</option> |
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7 <option value="yes">yes</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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8 </param> |
a6fdea25d41f
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9 <when value="no" /> |
a6fdea25d41f
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10 <when value="yes"> |
a6fdea25d41f
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11 <yield/> |
a6fdea25d41f
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12 </when> |
a6fdea25d41f
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13 </conditional> |
a6fdea25d41f
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14 </xml> |
a6fdea25d41f
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15 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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16 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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17 --extendReads $advancedOpt.extendReads |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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18 $advancedOpt.ignoreDuplicates |
a6fdea25d41f
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19 $advancedOpt.centerReads |
a6fdea25d41f
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20 #if $advancedOpt.minMappingQuality: |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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21 --minMappingQuality '$advancedOpt.minMappingQuality' |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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22 #end if |
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23 #if $advancedOpt.samFlagInclude: |
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24 --samFlagInclude $advancedOpt.samFlagInclude |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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25 #end if |
a6fdea25d41f
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26 #if $advancedOpt.samFlagExclude: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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27 --samFlagExclude $advancedOpt.samFlagExclude |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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28 #end if |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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29 </token> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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30 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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31 <xml name="heatmap_options"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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32 <expand macro="zMin_zMax" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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33 <expand macro="colorMap" /> |
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34 <expand macro="plotTitle" /> |
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35 <expand macro="plotNumbers" /> |
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36 </xml> |
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37 |
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38 <token name="@HEATMAP_OPTIONS@"> |
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39 #if $zMin: |
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40 --zMin $zMin |
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41 #end if |
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42 #if $zMax: |
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43 --zMax $zMax |
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44 #end if |
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45 --colorMap '$colorMap' |
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46 $plotNumbers |
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47 </token> |
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48 |
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49 <expand macro="plotTitle" /> |
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50 <expand macro="plotNumbers" /> |
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51 <conditional name="output"> |
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52 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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53 <option value="no" selected="true">no</option> |
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54 <option value="yes">yes</option> |
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55 </param> |
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56 <when value="no" /> |
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57 <when value="yes"> |
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58 <expand macro="input_image_file_format"/> |
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59 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/> |
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60 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/> |
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61 </when> |
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62 </conditional> |
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63 |
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64 <xml name="includeZeros"> |
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65 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
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66 label="Include zeros" |
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67 help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." /> |
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68 </xml> |
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69 |
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70 <xml name="zMin_zMax"> |
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71 <param argument="--zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities" |
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72 help="If not specified the value is set automatically."/> |
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73 <param argument="--zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities" |
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74 help="If not specified the value is set automatically."/> |
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75 </xml> |
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76 |
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77 <xml name="region_limit_operation"> |
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78 <param argument="--region" type="text" value="" |
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79 label="Region of the genome to limit the operation to" |
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80 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> |
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81 </xml> |
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82 |
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83 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
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84 <token name="@WRAPPER_VERSION@">2.0.0</token> |
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85 <xml name="requirements"> |
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86 <requirements> |
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87 <requirement type="package" version="2.7.10">python</requirement> |
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88 <requirement type="binary">@BINARY@</requirement> |
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89 <requirement type="package" version="2.0">deepTools</requirement> |
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90 <yield /> |
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91 </requirements> |
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92 <expand macro="stdio" /> |
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93 <version_command>@BINARY@ --version</version_command> |
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94 </xml> |
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95 |
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96 <xml name="smoothLength"> |
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97 <param argument="--smoothLength" type="integer" value="" optional="True" min="1" |
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98 label="Smooth values using the following length (in bp)" |
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99 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> |
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100 </xml> |
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101 |
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102 |
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103 <xml name="kmeans_clustering"> |
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104 <conditional name="used_multiple_regions"> |
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105 <param name="used_multiple_regions_options" type="select" |
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106 label="Did you compute the matrix with more than one groups of regions?" |
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107 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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108 <option value="yes">Yes, I used multiple groups of regions</option> |
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109 <option value="no">No, I used only one group</option> |
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110 </param> |
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111 <when value="no"> |
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112 <conditional name="clustering"> |
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113 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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114 <option value="none">No clustering</option> |
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115 <option value="kmeans">Kmeans clustering</option> |
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116 </param> |
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117 <when value="kmeans"> |
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118 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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119 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/> |
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120 </when> |
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121 <when value="none" /> |
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122 </conditional> |
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123 </when> |
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124 <when value="yes" /> |
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125 </conditional> |
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126 </xml> |
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127 |
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128 <token name="@KMEANS_CLUSTERING@"> |
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129 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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130 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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131 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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132 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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133 #end if |
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134 #end if |
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135 #end if |
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136 </token> |
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137 |
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138 <xml name="samFlags"> |
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139 <param argument="--samFlagInclude" type="integer" optional="True" value="" |
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140 label="Include reads based on the SAM flag" |
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141 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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142 <param argument="--samFlagExclude" type="integer" optional="True" value="" |
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143 label="Exclude reads based on the SAM flag" |
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144 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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145 </xml> |
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146 |
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147 <xml name="read_processing_options"> |
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148 <expand macro="extendReads" /> |
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149 <expand macro="ignoreDuplicates" /> |
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150 <expand macro="centerReads" /> |
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151 <expand macro="minMappingQuality" /> |
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152 <expand macro="samFlags" /> |
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153 </xml> |
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154 |
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155 <xml name="plotNumbers"> |
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156 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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157 label="Plot the correlation value" |
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158 help="If set, then the correlation number is plotted on top of the heatmap."/> |
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159 </xml> |
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160 |
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161 <xml name="extendReads"> |
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162 <param argument="--extendReads" type="integer" value="" optional="True" |
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163 label="Extend reads to the given average fragment size" |
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164 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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165 By default *each* read mate is extended. |
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166 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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167 Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value. |
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168 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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169 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."/> |
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170 </xml> |
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171 |
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172 <xml name="corMethod"> |
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173 <param argument="--corMethod" type="select" label="Correlation method"> |
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174 <option value="spearman" selected="True">Spearman</option> |
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175 <option value="pearson">Pearson</option> |
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176 </param> |
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177 </xml> |
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178 |
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179 <xml name="distanceBetweenBins"> |
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180 <param argument="--distanceBetweenBins" type="integer" value="0" min="0" |
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181 label="Distance between bins" |
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182 help="By default, bamCorrelate considers consecutive bins of |
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183 the specified 'Bin size'. However, to reduce the |
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184 computation time, a larger distance between bins can |
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185 by given. Larger distances result in less bins being |
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186 considered."/> |
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187 </xml> |
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188 |
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189 <xml name="centerReads"> |
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190 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" |
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191 label="Center regions with respect to the fragment length" |
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192 help="For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. "/> |
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193 </xml> |
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194 |
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195 <xml name="ignoreDuplicates"> |
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196 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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197 label="Ignore duplicates" |
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198 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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199 </xml> |
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200 |
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201 <xml name="sortUsing"> |
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202 <param argument="--sortUsing" type="select" label="Method used for sorting" |
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203 help="For each row the method is computed."> |
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204 <option value="mean" selected="true">mean</option> |
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205 <option value="median">median</option> |
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206 <option value="min">min</option> |
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207 <option value="max">max</option> |
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208 <option value="sum">sum</option> |
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209 <option value="region_length">region length</option> |
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210 </param> |
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211 </xml> |
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212 |
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213 <xml name="sortRegions"> |
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214 <param argument="--sortRegions" type="select" label="Sort regions" |
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215 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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216 <option value="no">no ordering</option> |
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217 <option value="descend" selected="true">descending order</option> |
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218 <option value="ascend">ascending order</option> |
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219 </param> |
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220 </xml> |
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221 |
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222 <xml name="minMappingQuality"> |
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223 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1" |
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224 label="Minimum mapping quality" |
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225 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> |
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226 </xml> |
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227 |
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228 <xml name="skipZeros"> |
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229 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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230 label ="Skip zeros" |
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231 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." /> |
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232 </xml> |
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233 |
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234 <xml name="fragmentLength"> |
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235 <param argument="--fragmentLength" type="integer" value="300" min="1" |
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236 label="Fragment length used for the sequencing" |
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237 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/> |
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238 </xml> |
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239 |
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240 <xml name="scaleFactor"> |
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241 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" |
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242 help="When used in combination with --normalizeTo1x or |
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243 --normalizeUsingRPKM, the computed scaling factor will |
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244 be multiplied by the given scale factor." /> |
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245 </xml> |
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246 |
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247 <xml name="scaleFactors"> |
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248 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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249 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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250 </xml> |
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251 |
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252 <xml name="stdio"> |
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253 <stdio> |
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254 <exit_code range="1:" /> |
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255 <exit_code range=":-1" /> |
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256 <regex match="Error:" /> |
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257 <regex match="Exception:" /> |
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258 <regex match="EXception:" /> |
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259 <regex match="Traceback" /> |
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260 </stdio> |
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261 </xml> |
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262 |
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263 <xml name="pseudocount"> |
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264 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
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265 </xml> |
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266 |
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267 <token name="@REFERENCES@"> |
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268 |
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269 .. class:: infomark |
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270 |
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271 For more information on the tools, please visit our `help site`_. |
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272 |
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273 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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274 |
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275 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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276 |
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277 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ |
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278 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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279 .. _help site: https://github.com/fidelram/deepTools/wiki/ |
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280 |
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281 </token> |
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282 <xml name="citations"> |
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283 <citations> |
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284 <citation type="doi">10.1093/nar/gku365</citation> |
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285 <yield /> |
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286 </citations> |
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287 </xml> |
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288 |
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289 <xml name="multiple_input_bams"> |
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290 <param argument="--bamfiles" type="data" format="bam" |
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291 label="Bam file" multiple="true" |
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292 help="The BAM file must be sorted."/> |
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293 </xml> |
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294 |
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295 <xml name="multiple_input_bigwigs"> |
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296 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" |
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297 label="Bigwig file" |
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298 help="The Bigwig file must be sorted."/> |
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299 </xml> |
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300 |
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301 <xml name="plotTitle"> |
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302 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
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303 label="Title of the plot" |
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304 help="Title of the plot, to be printed on top of the generated image." /> |
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305 </xml> |
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306 |
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307 <token name="@multiple_input_bams@"> |
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308 <![CDATA[ |
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309 #set files=[] |
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310 #set labels=[] |
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311 #for $counter, $bamfile in enumerate($bamfiles): |
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312 ln -s "${bamfile}" "./${counter}.bam" && |
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313 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && |
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314 #silent $files.append('%s.bam' % $counter) |
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315 #silent $labels.append('%s' % ($bamfile.display_name)) |
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316 #end for |
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317 ]]> |
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318 </token> |
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319 |
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320 <token name="@multiple_input_bigwigs@"> |
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321 <![CDATA[ |
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322 #set files=[] |
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323 #set labels=[] |
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324 #for $counter, $bigwig in enumerate($bigwigfiles): |
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325 ln -s "${bigwig}" "${counter}.bw" && |
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326 #silent $files.append('%s.bw' % $counter) |
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327 #silent $labels.append('%s' % ($bigwig.display_name)) |
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328 #end for |
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329 ]]> |
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330 </token> |
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331 |
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332 <xml name="reference_genome_source"> |
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333 <conditional name="source"> |
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334 <param name="ref_source" type="select" label="Reference genome"> |
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335 <option value="cached">locally cached</option> |
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336 <option value="history">in your history</option> |
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337 </param> |
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338 <when value="cached"> |
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339 <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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340 <options from_data_table="lastz_seqs"> |
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341 <filter type="sort_by" column="1" /> |
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342 <validator type="no_options" message="No indexes are available." /> |
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343 </options> |
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344 </param> |
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345 </when> |
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346 <when value="history"> |
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347 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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348 </when> |
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349 </conditional> |
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350 </xml> |
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351 |
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352 <token name="@reference_genome_source@"> |
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353 #if $source.ref_source=="history": |
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354 --genome $source.input1 |
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355 #else: |
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356 --genome "${source.input1_2bit.fields.path}" |
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357 #end if |
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358 </token> |
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359 |
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360 <xml name="effectiveGenomeSize"> |
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361 <conditional name="effectiveGenomeSize"> |
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362 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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363 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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364 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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365 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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366 <option value="93260000">ce10 (93260000)</option> |
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367 <option value="121400000">dm3 (121400000)</option> |
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368 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
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369 <option value="2150570000">mm9 (2150570000)</option> |
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370 <option value="specific">user specified</option> |
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371 </param> |
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372 <when value="specific"> |
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373 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> |
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374 </when> |
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375 <when value="2150570000" /> |
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376 <when value="2451960000" /> |
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377 <when value="121400000" /> |
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378 <when value="93260000" /> |
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379 </conditional> |
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380 </xml> |
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381 |
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382 <xml name="image_file_format"> |
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383 <param argument="--outFileFormat" type="select" label="Image file format"> |
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384 <option value="png" selected="true">png</option> |
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385 <option value="pdf">pdf</option> |
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386 <option value="svg">svg</option> |
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387 <option value="eps">eps</option> |
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388 </param> |
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389 </xml> |
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390 |
1
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391 <xml name="skipNAs"> |
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392 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" |
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393 label="Ignore missing data?" |
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394 help="This parameter determines if non-covered regions |
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395 (regions without overlapping reads) in a bam/bigWig file |
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396 should be skipped. The default is to treat those |
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397 regions as having a value of zero. The decision to |
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398 skip non-covered regions depends on the interpretation |
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399 of the data. Non-covered regions may represent for |
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400 example repetitive regions that want to be skipped. |
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401 (default: False)" /> |
0
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402 </xml> |
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403 |
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404 <xml name="input_save_matrix_values"> |
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405 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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406 </xml> |
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407 |
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408 <xml name="input_graphic_output_settings"> |
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409 <conditional name="output" > |
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410 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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411 <option value="no" selected="true">no</option> |
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412 <option value="yes">yes</option> |
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413 </param> |
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414 <when value="no" /> |
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415 <when value="yes"> |
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416 <yield /> |
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417 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> |
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418 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
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419 </when> |
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420 </conditional> |
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421 </xml> |
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422 |
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423 <xml name="input_image_file_format"> |
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424 <param name="outFileFormat" type="select" label="Image file format"> |
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425 <option value="png" selected="true">png</option> |
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426 <option value="pdf">pdf</option> |
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427 <option value="svg">svg</option> |
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428 <option value="eps">eps</option> |
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429 <option value="emf">emf</option> |
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430 </param> |
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431 </xml> |
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432 |
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433 <xml name="output_image_file_format"> |
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434 <data format="png" name="outFileName" label="${tool.name} image"> |
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435 <change_format> |
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436 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
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437 <when input="output.outFileFormat" value="svg" format="svg" /> |
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438 <when input="output.outFileFormat" value="eps" format="eps" /> |
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439 <when input="output.outFileFormat" value="emf" format="emf" /> |
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440 </change_format> |
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441 </data> |
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442 </xml> |
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443 |
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444 <xml name="output_save_matrix_values"> |
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445 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
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446 <filter> |
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447 (( |
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448 output['showOutputSettings'] == 'yes' and |
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449 output['saveMatrix'] is True |
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450 )) |
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451 </filter> |
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452 </data> |
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453 </xml> |
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454 |
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455 <xml name="output_graphic_outputs"> |
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456 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
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457 <filter> |
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458 (( |
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459 output['showOutputSettings'] == 'yes' and |
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460 output['saveData'] is True |
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461 )) |
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462 </filter> |
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463 </data> |
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464 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
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465 <filter> |
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466 (( |
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467 output['showOutputSettings'] == 'yes' and |
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468 output['saveSortedRegions'] is True |
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469 )) |
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470 </filter> |
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471 </data> |
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472 </xml> |
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473 |
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474 <xml name="colorMap"> |
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475 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/"> |
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476 <option value="RdYlBu" selected="true">RdYlBu</option> |
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477 <option value="Accent">Accent</option> |
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478 <option value="Spectral">Spectral</option> |
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479 <option value="Set1">Set1</option> |
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480 <option value="Set2">Set2</option> |
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481 <option value="Set3">Set3</option> |
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482 <option value="Dark2">Dark2</option> |
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483 <option value="Reds">Reds</option> |
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484 <option value="Oranges">Oranges</option> |
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485 <option value="Greens">Greens</option> |
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486 <option value="Blues">Blues</option> |
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487 <option value="Greys">Greys</option> |
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488 <option value="Purples">Purples</option> |
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489 <option value="Paired">Paired</option> |
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490 <option value="Pastel1">Pastel1</option> |
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491 <option value="Pastel2">Pastel2</option> |
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492 <option value="spring">spring</option> |
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493 <option value="summer">summer</option> |
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494 <option value="autumn">autumn</option> |
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495 <option value="winter">winter</option> |
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496 <option value="hot">hot</option> |
a6fdea25d41f
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497 <option value="coolwarm">coolwarm</option> |
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498 <option value="cool">cool</option> |
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499 <option value="seismic">seismic</option> |
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500 <option value="terrain">terrain</option> |
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501 <option value="ocean">ocean</option> |
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502 <option value="rainbow">rainbow</option> |
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503 <option value="bone">bone</option> |
a6fdea25d41f
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504 <option value="flag">flag</option> |
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505 <option value="prism">prism</option> |
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506 <option value="cubehelix">cubehelix</option> |
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507 <option value="binary">binary</option> |
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508 <option value="pink">pink</option> |
a6fdea25d41f
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509 <option value="gray">gray</option> |
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510 <option value="copper">copper</option> |
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511 <option value="BrBG">BrBG</option> |
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512 <option value="BuGn">BuGn</option> |
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513 <option value="BuPu">BuPu</option> |
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514 <option value="GnBu">GnBu</option> |
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515 <option value="OrRd">OrRd</option> |
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516 <option value="PiYG">PiYG</option> |
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517 <option value="PRGn">PRGn</option> |
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518 <option value="PuOr">PuOr</option> |
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519 <option value="PuRd">PuRd</option> |
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520 <option value="PuBu">PuBu</option> |
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521 <option value="RdBu">RdBu</option> |
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522 <option value="RdGy">RdGy</option> |
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523 <option value="RdPu">RdPu</option> |
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524 <option value="YlGn">YlGn</option> |
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525 <option value="PuBuGn">PuBuGn</option> |
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526 <option value="RdYlGn">RdYlGn</option> |
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527 <option value="YlGnBu">YlGnBu</option> |
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528 <option value="YlOrBr">YlOrBr</option> |
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529 <option value="YlOrRd">YlOrRd</option> |
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530 <option value="gist_gray">gist_gray</option> |
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531 <option value="gist_stern">gist_stern</option> |
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532 <option value="gist_earth">gist_earth</option> |
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diff
changeset
|
533 <option value="gist_yarg">gist_yarg</option> |
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534 <option value="gist_ncar">gist_ncar</option> |
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535 <option value="gist_rainbow">gist_rainbow</option> |
a6fdea25d41f
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536 <option value="gist_heat">gist_heat</option> |
a6fdea25d41f
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537 <option value="gnuplot">gnuplot</option> |
a6fdea25d41f
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|
538 <option value="gnuplot2">gnuplot2</option> |
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539 <option value="CMRmap">CMRmap</option> |
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540 <option value="bwr">bwr</option> |
a6fdea25d41f
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541 <option value="hsv">hsv</option> |
a6fdea25d41f
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542 <option value="brg">brg</option> |
a6fdea25d41f
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543 <option value="jet">jet</option> |
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544 <option value="afmhot">afmhot</option> |
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545 <option value="Accent_r">Accent reversed</option> |
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546 <option value="Spectral_r">Spectral reversed</option> |
a6fdea25d41f
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547 <option value="Set1_r">Set1 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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548 <option value="Set2_r">Set2 reversed</option> |
a6fdea25d41f
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549 <option value="Set3_r">Set3 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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550 <option value="Dark2_r">Dark2 reversed</option> |
a6fdea25d41f
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551 <option value="Reds_r">Reds reversed</option> |
a6fdea25d41f
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552 <option value="Oranges_r">Oranges reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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553 <option value="Greens_r">Greens reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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554 <option value="Blues_r">Blues reversed</option> |
a6fdea25d41f
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555 <option value="Greys_r">Greys reversed</option> |
a6fdea25d41f
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changeset
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556 <option value="Purples_r">Purples reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
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557 <option value="Paired_r">Paired reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
|
558 <option value="Pastel1_r">Pastel1 reversed</option> |
a6fdea25d41f
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changeset
|
559 <option value="Pastel2_r">Pastel2 reversed</option> |
a6fdea25d41f
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560 <option value="spring_r">spring reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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561 <option value="summer_r">summer reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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562 <option value="autumn_r">autumn reversed</option> |
a6fdea25d41f
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|
563 <option value="winter_r">winter reversed</option> |
a6fdea25d41f
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564 <option value="hot_r">hot reversed</option> |
a6fdea25d41f
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565 <option value="coolwarm_r">coolwarm reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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566 <option value="cool_r">cool reversed</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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567 <option value="seismic_r">seismic reversed</option> |
a6fdea25d41f
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568 <option value="terrain_r">terrain reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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569 <option value="ocean_r">ocean reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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570 <option value="rainbow_r">rainbow reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff
changeset
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571 <option value="bone_r">bone reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
|
572 <option value="flag_r">flag reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
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573 <option value="prism_r">prism reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
|
574 <option value="cubehelix_r">cubehelix reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
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575 <option value="binary_r">binary reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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diff
changeset
|
576 <option value="pink_r">pink reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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577 <option value="gray_r">gray reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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578 <option value="copper_r">copper reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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579 <option value="BrBG_r">BrBG reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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580 <option value="BuGn_r">BuGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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581 <option value="BuPu_r">BuPu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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582 <option value="GnBu_r">GnBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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583 <option value="OrRd_r">OrRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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584 <option value="PiYG_r">PiYG reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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585 <option value="PRGn_r">PRGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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586 <option value="PuOr_r">PuOr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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587 <option value="PuRd_r">PuRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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588 <option value="PuBu_r">PuBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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589 <option value="RdBu_r">RdBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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590 <option value="RdGy_r">RdGy reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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591 <option value="RdPu_r">RdPu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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592 <option value="YlGn_r">YlGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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593 <option value="PuBuGn_r">PuBuGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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594 <option value="RdYlBu_r">RdYlBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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595 <option value="RdYlGn_r">RdYlGn reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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596 <option value="YlGnBu_r">YlGnBu reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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597 <option value="YlOrBr_r">YlOrBr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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598 <option value="YlOrRd_r">YlOrRd reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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599 <option value="gist_gray_r">gist_gray reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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600 <option value="gist_stern_r">gist_stern reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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601 <option value="gist_earth_r">gist_earth reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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602 <option value="gist_yarg_r">gist_yarg reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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changeset
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603 <option value="gist_ncar_r">gist_ncar reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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604 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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605 <option value="gist_heat_r">gist_heat reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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606 <option value="gnuplot_r">gnuplot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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607 <option value="gnuplot2_r">gnuplot2 reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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608 <option value="CMRmap_r">CMRmap reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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609 <option value="bwr_r">bwr reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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610 <option value="hsv_r">hsv reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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611 <option value="brg_r">brg reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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612 <option value="jet_r">jet reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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613 <option value="afmhot_r">afmhot reversed</option> |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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614 </param> |
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615 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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616 </xml> |
a6fdea25d41f
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617 |
a6fdea25d41f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
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618 </macros> |