annotate deepTools_macros.xml @ 17:ef65d6b68ccc draft

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author bgruening
date Sat, 21 Dec 2013 14:26:06 -0500
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1 <macros>
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2 <xml name="bamCorrelate_mode_actions">
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3 <conditional name="advancedOpt">
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4 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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5 <option value="no" selected="true">no</option>
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6 <option value="yes">yes</option>
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7 </param>
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8 <when value="no" />
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9 <when value="yes">
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10 <param name="region" type="text" value=""
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11 label="Region of the genome to limit the operation to"
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12 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
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14 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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15 label="Do not extend paired ends"
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16 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
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18 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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19 label="Ignore duplicates"
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20 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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21
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22 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
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23 label="Minimum mapping quality"
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24 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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26 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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27 label ="Include zeros"
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28 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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29
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30 <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
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31 help="If not specified the value is set automatically."/>
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32
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33 <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
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34 help="If not specified the value is set automatically."/>
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35
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36 <expand macro="colormap" />
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37 </when>
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38 </conditional>
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39 </xml>
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40 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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41 <xml name="requirements">
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42 <requirements>
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43 <requirement type="package" >samtools</requirement>
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44 <requirement type="package" >deepTools</requirement>
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45 <requirement type="package" >ucsc_tools</requirement>
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46 <requirement type="package" version="1.5.4_e5c75f3e967be0fa1d6dbcbb63a0f992e1cdcd61">deepTools</requirement>
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47 <requirement type="package" version="0.1">ucsc_tools</requirement>
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48 <requirement type="package" version="1.7.1">numpy</requirement>
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49 <requirement type="package" version="0.7.7">pysam</requirement>
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50 <requirement type="package" version="0.12.0">scipy</requirement>
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51 <requirement type="package" version="1.2.1">matplotlib</requirement>
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52 <requirement type="package" version="0.1.19">samtools</requirement>
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53 <requirement type="package" version="12-2013">bx-python</requirement>
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54 <yield />
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55 </requirements>
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56 </xml>
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57 <xml name="stdio">
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58 <stdio>
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59 <exit_code range="1:" />
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60 <exit_code range=":-1" />
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61 <regex match="Error:" />
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62 <regex match="Exception:" />
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63 <regex match="EXception:" />
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64 <regex match="Traceback" />
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65 </stdio>
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66 </xml>
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67 <token name="@REFERENCES@">
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68
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69 For more informations, please visit our `project site`_.
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70
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71 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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72
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73 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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74
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75
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76 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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77 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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78 .. _project site: https://github.com/fidelram/deepTools
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79
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80 </token>
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81
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82 <xml name="multiple_input_bams">
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83 <repeat name="input_files" title="BAM files" min="2">
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84 <param name="bamfile" type="data" format="bam"
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85 label="Bam file"
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86 help="The BAM file must be sorted."/>
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87 <param name="label" type="text" size="30" optional="true" value=""
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88 label="Label"
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89 help="Label to use in the output. If not given the dataset name will be used instead."/>
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90 </repeat>
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91 </xml>
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93 <token name="@multiple_input_bams@">
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94 #import tempfile
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95 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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96 #set files=[]
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97 #set labels=[]
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98 #for $i in $input_files:
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99 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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100 #set $temp_input_path = $temp_input_handle.name
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101 #silent $temp_input_handle.close()
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102 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
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103 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
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104 #silent $files.append('%s.bam' % $temp_input_path)
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105
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106 ##set $files += [str($i.bamfile)]
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107 #if str($i.label.value) != "":
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108 #set $labels += ["\"%s\"" % ($i.label.value)]
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109 #else
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110 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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111 #end if
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112 #end for
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113 </token>
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114
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115 <xml name="reference_genome_source">
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116 <conditional name="source">
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117 <param name="ref_source" type="select" label="Reference genome">
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118 <option value="cached">locally cached</option>
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119 <option value="history">in your history</option>
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120 </param>
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121 <when value="cached">
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122 <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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123 <options from_data_table="deepTools_seqs">
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124 <filter type="sort_by" column="1" />
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125 <validator type="no_options" message="No indexes are available." />
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126 </options>
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127 </param>
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128 </when>
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129 <when value="history">
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130 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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131 </when>
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132 </conditional>
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133 </xml>
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134
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135 <token name="@reference_genome_source@">
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136 #if $source.ref_source=="history":
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137 --genome $source.input1
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138 #else:
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139 --genome "${source.input1_2bit.fields.path}"
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140 #end if
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141 </token>
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142
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143 <xml name="effectiveGenomeSize">
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144 <conditional name="effectiveGenomeSize">
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145 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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146 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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147 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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148 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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149 <option value="2150570000">mm9</option>
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150 <option value="2451960000">hg19</option>
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151 <option value="121400000">dm3</option>
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152 <option value="93260000">ce10</option>
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153 <option value="specific">user specified</option>
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154 </param>
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155 <when value="specific">
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156 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
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157 </when>
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158 </conditional>
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159 </xml>
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160
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161 <xml name="image_file_format">
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162 <param name="outFileFormat" type="select" label="Image file format">
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163 <option value="png" selected="true">png</option>
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164 <option value="pdf">pdf</option>
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165 <option value="svg">svg</option>
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166 <option value="eps">eps</option>
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167 <option value="emf">emf</option>
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168 </param>
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169 </xml>
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170
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171 <xml name="input_save_matrix_values">
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172 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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173 </xml>
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174
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175 <xml name="input_graphic_output_settings">
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176 <conditional name="output" >
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177 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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178 <option value="no" selected="true">no</option>
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179 <option value="yes">yes</option>
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180 </param>
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181 <when value="no" />
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182 <when value="yes">
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183 <yield />
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184 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
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185 <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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parents:
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186 </when>
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parents:
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187 </conditional>
13
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188 </xml>
0
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parents:
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189
13
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diff changeset
190 <xml name="input_image_file_format">
11
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parents: 10
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191 <param name="outFileFormat" type="select" label="Image file format">
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parents: 10
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192 <option value="png" selected="true">png</option>
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parents: 10
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193 <option value="pdf">pdf</option>
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parents: 10
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194 <option value="svg">svg</option>
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parents: 10
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195 <option value="eps">eps</option>
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parents: 10
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196 <option value="emf">emf</option>
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parents: 10
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197 </param>
13
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parents: 12
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198 </xml>
11
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199
13
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parents: 12
diff changeset
200 <xml name="output_image_file_format">
10
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parents: 9
diff changeset
201 <data format="png" name="outFileName" label="${tool.name} image">
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parents: 9
diff changeset
202 <change_format>
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parents: 9
diff changeset
203 <when input="output.outFileFormat" value="pdf" format="pdf" />
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parents: 9
diff changeset
204 <when input="output.outFileFormat" value="svg" format="svg" />
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parents: 9
diff changeset
205 <when input="output.outFileFormat" value="eps" format="eps" />
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parents: 9
diff changeset
206 <when input="output.outFileFormat" value="emf" format="emf" />
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parents: 9
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207 </change_format>
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parents: 9
diff changeset
208 </data>
13
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parents: 12
diff changeset
209 </xml>
11
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parents: 10
diff changeset
210
13
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parents: 12
diff changeset
211 <xml name="output_save_matrix_values">
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parents: 12
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212 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
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parents: 12
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213 <filter>
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parents: 12
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214 ((
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parents: 12
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215 output['showOutputSettings'] == 'yes' and
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parents: 12
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216 output['saveMatrix'] is True
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parents: 12
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217 ))
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parents: 12
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218 </filter>
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parents: 12
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219 </data>
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parents: 12
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220 </xml>
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parents: 12
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221
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parents: 12
diff changeset
222 <xml name="output_graphic_outputs">
10
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parents: 9
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223 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
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parents: 9
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224 <filter>
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parents: 9
diff changeset
225 ((
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parents: 9
diff changeset
226 output['showOutputSettings'] == 'yes' and
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parents: 9
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227 output['saveData'] is True
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parents: 9
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228 ))
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parents: 9
diff changeset
229 </filter>
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parents: 9
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230 </data>
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parents: 9
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231 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
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parents: 9
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232 <filter>
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parents: 9
diff changeset
233 ((
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parents: 9
diff changeset
234 output['showOutputSettings'] == 'yes' and
135f3bae5c56 Uploaded
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parents: 9
diff changeset
235 output['saveSortedRegions'] is True
135f3bae5c56 Uploaded
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parents: 9
diff changeset
236 ))
135f3bae5c56 Uploaded
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parents: 9
diff changeset
237 </filter>
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parents: 9
diff changeset
238 </data>
13
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parents: 12
diff changeset
239 </xml>
10
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parents: 9
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240
13
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parents: 12
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241 <xml name="colormap">
0
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parents:
diff changeset
242 <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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parents:
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243 <option value="RdYlBu" selected="true">RdYlBu</option>
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parents:
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244 <option value="Accent">Accent</option>
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parents:
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245 <option value="Spectral">Spectral</option>
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parents:
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246 <option value="Set1">Set1</option>
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parents:
diff changeset
247 <option value="Set2">Set2</option>
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parents:
diff changeset
248 <option value="Set3">Set3</option>
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parents:
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249 <option value="Dark2">Dark2</option>
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parents:
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250 <option value="Reds">Reds</option>
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parents:
diff changeset
251 <option value="Oranges">Oranges</option>
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parents:
diff changeset
252 <option value="Greens">Greens</option>
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parents:
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253 <option value="Blues">Blues</option>
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parents:
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254 <option value="Greys">Greys</option>
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parents:
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255 <option value="Purples">Purples</option>
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parents:
diff changeset
256 <option value="Paired">Paired</option>
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parents:
diff changeset
257 <option value="Pastel1">Pastel1</option>
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parents:
diff changeset
258 <option value="Pastel2">Pastel2</option>
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parents:
diff changeset
259 <option value="spring">spring</option>
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parents:
diff changeset
260 <option value="summer">summer</option>
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parents:
diff changeset
261 <option value="autumn">autumn</option>
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parents:
diff changeset
262 <option value="winter">winter</option>
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parents:
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263 <option value="hot">hot</option>
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parents:
diff changeset
264 <option value="coolwarm">coolwarm</option>
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parents:
diff changeset
265 <option value="cool">cool</option>
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parents:
diff changeset
266 <option value="seismic">seismic</option>
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parents:
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267 <option value="terrain">terrain</option>
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parents:
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268 <option value="ocean">ocean</option>
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parents:
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269 <option value="rainbow">rainbow</option>
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parents:
diff changeset
270 <option value="bone">bone</option>
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parents:
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271 <option value="flag">flag</option>
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parents:
diff changeset
272 <option value="prism">prism</option>
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parents:
diff changeset
273 <option value="cubehelix">cubehelix</option>
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parents:
diff changeset
274 <option value="binary">binary</option>
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parents:
diff changeset
275 <option value="pink">pink</option>
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parents:
diff changeset
276 <option value="gray">gray</option>
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parents:
diff changeset
277 <option value="copper">copper</option>
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parents:
diff changeset
278 <option value="BrBG">BrBG</option>
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parents:
diff changeset
279 <option value="BuGn">BuGn</option>
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parents:
diff changeset
280 <option value="BuPu">BuPu</option>
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parents:
diff changeset
281 <option value="GnBu">GnBu</option>
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parents:
diff changeset
282 <option value="OrRd">OrRd</option>
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parents:
diff changeset
283 <option value="PiYG">PiYG</option>
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parents:
diff changeset
284 <option value="PRGn">PRGn</option>
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parents:
diff changeset
285 <option value="PuOr">PuOr</option>
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parents:
diff changeset
286 <option value="PuRd">PuRd</option>
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parents:
diff changeset
287 <option value="PuBu">PuBu</option>
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parents:
diff changeset
288 <option value="RdBu">RdBu</option>
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parents:
diff changeset
289 <option value="RdGy">RdGy</option>
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parents:
diff changeset
290 <option value="RdPu">RdPu</option>
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parents:
diff changeset
291 <option value="YlGn">YlGn</option>
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parents:
diff changeset
292 <option value="PuBuGn">PuBuGn</option>
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parents:
diff changeset
293 <option value="RdYlGn">RdYlGn</option>
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parents:
diff changeset
294 <option value="YlGnBu">YlGnBu</option>
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parents:
diff changeset
295 <option value="YlOrBr">YlOrBr</option>
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parents:
diff changeset
296 <option value="YlOrRd">YlOrRd</option>
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parents:
diff changeset
297 <option value="gist_gray">gist_gray</option>
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parents:
diff changeset
298 <option value="gist_stern">gist_stern</option>
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parents:
diff changeset
299 <option value="gist_earth">gist_earth</option>
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parents:
diff changeset
300 <option value="gist_yarg">gist_yarg</option>
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parents:
diff changeset
301 <option value="gist_ncar">gist_ncar</option>
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parents:
diff changeset
302 <option value="gist_rainbow">gist_rainbow</option>
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parents:
diff changeset
303 <option value="gist_heat">gist_heat</option>
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parents:
diff changeset
304 <option value="gnuplot">gnuplot</option>
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parents:
diff changeset
305 <option value="gnuplot2">gnuplot2</option>
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parents:
diff changeset
306 <option value="CMRmap">CMRmap</option>
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parents:
diff changeset
307 <option value="bwr">bwr</option>
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parents:
diff changeset
308 <option value="hsv">hsv</option>
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parents:
diff changeset
309 <option value="brg">brg</option>
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parents:
diff changeset
310 <option value="jet">jet</option>
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parents:
diff changeset
311 <option value="afmhot">afmhot</option>
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parents:
diff changeset
312 <option value="Accent_r">Accent reversed</option>
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parents:
diff changeset
313 <option value="Spectral_r">Spectral reversed</option>
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parents:
diff changeset
314 <option value="Set1_r">Set1 reversed</option>
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parents:
diff changeset
315 <option value="Set2_r">Set2 reversed</option>
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parents:
diff changeset
316 <option value="Set3_r">Set3 reversed</option>
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parents:
diff changeset
317 <option value="Dark2_r">Dark2 reversed</option>
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parents:
diff changeset
318 <option value="Reds_r">Reds reversed</option>
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parents:
diff changeset
319 <option value="Oranges_r">Oranges reversed</option>
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parents:
diff changeset
320 <option value="Greens_r">Greens reversed</option>
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parents:
diff changeset
321 <option value="Blues_r">Blues reversed</option>
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parents:
diff changeset
322 <option value="Greys_r">Greys reversed</option>
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parents:
diff changeset
323 <option value="Purples_r">Purples reversed</option>
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parents:
diff changeset
324 <option value="Paired_r">Paired reversed</option>
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parents:
diff changeset
325 <option value="Pastel1_r">Pastel1 reversed</option>
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parents:
diff changeset
326 <option value="Pastel2_r">Pastel2 reversed</option>
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parents:
diff changeset
327 <option value="spring_r">spring reversed</option>
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parents:
diff changeset
328 <option value="summer_r">summer reversed</option>
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parents:
diff changeset
329 <option value="autumn_r">autumn reversed</option>
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parents:
diff changeset
330 <option value="winter_r">winter reversed</option>
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parents:
diff changeset
331 <option value="hot_r">hot reversed</option>
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parents:
diff changeset
332 <option value="coolwarm_r">coolwarm reversed</option>
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parents:
diff changeset
333 <option value="cool_r">cool reversed</option>
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parents:
diff changeset
334 <option value="seismic_r">seismic reversed</option>
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parents:
diff changeset
335 <option value="terrain_r">terrain reversed</option>
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parents:
diff changeset
336 <option value="ocean_r">ocean reversed</option>
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parents:
diff changeset
337 <option value="rainbow_r">rainbow reversed</option>
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parents:
diff changeset
338 <option value="bone_r">bone reversed</option>
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parents:
diff changeset
339 <option value="flag_r">flag reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
340 <option value="prism_r">prism reversed</option>
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parents:
diff changeset
341 <option value="cubehelix_r">cubehelix reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
342 <option value="binary_r">binary reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
343 <option value="pink_r">pink reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
344 <option value="gray_r">gray reversed</option>
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parents:
diff changeset
345 <option value="copper_r">copper reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
346 <option value="BrBG_r">BrBG reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
347 <option value="BuGn_r">BuGn reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
348 <option value="BuPu_r">BuPu reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
349 <option value="GnBu_r">GnBu reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
350 <option value="OrRd_r">OrRd reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
351 <option value="PiYG_r">PiYG reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
352 <option value="PRGn_r">PRGn reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
353 <option value="PuOr_r">PuOr reversed</option>
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parents:
diff changeset
354 <option value="PuRd_r">PuRd reversed</option>
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parents:
diff changeset
355 <option value="PuBu_r">PuBu reversed</option>
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parents:
diff changeset
356 <option value="RdBu_r">RdBu reversed</option>
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parents:
diff changeset
357 <option value="RdGy_r">RdGy reversed</option>
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parents:
diff changeset
358 <option value="RdPu_r">RdPu reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
359 <option value="YlGn_r">YlGn reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
360 <option value="PuBuGn_r">PuBuGn reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
361 <option value="RdYlBu_r">RdYlBu reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
362 <option value="RdYlGn_r">RdYlGn reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
363 <option value="YlGnBu_r">YlGnBu reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
364 <option value="YlOrBr_r">YlOrBr reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
365 <option value="YlOrRd_r">YlOrRd reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
366 <option value="gist_gray_r">gist_gray reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
367 <option value="gist_stern_r">gist_stern reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
368 <option value="gist_earth_r">gist_earth reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
369 <option value="gist_yarg_r">gist_yarg reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
370 <option value="gist_ncar_r">gist_ncar reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
371 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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parents:
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372 <option value="gist_heat_r">gist_heat reversed</option>
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parents:
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373 <option value="gnuplot_r">gnuplot reversed</option>
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parents:
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374 <option value="gnuplot2_r">gnuplot2 reversed</option>
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parents:
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375 <option value="CMRmap_r">CMRmap reversed</option>
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parents:
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376 <option value="bwr_r">bwr reversed</option>
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parents:
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377 <option value="hsv_r">hsv reversed</option>
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parents:
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378 <option value="brg_r">brg reversed</option>
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parents:
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379 <option value="jet_r">jet reversed</option>
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parents:
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380 <option value="afmhot_r">afmhot reversed</option>
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parents:
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381 </param>
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parents:
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382
13
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parents: 12
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383 </xml>
0
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parents:
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384
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parents:
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385 </macros>