annotate circgraph.xml @ 0:ef5f8bbf7730 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
author iuc
date Wed, 09 Aug 2017 09:52:52 -0400
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ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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1 <?xml version="1.0"?>
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2 <tool id="circgraph" name="Circos Builder" version="@WRAPPER_VERSION@">
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3 <description>creates circos plots from standard bioinformatics datatypes.</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>macros_conffiles.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <version_command>circos --version</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 ## Directory structure
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12 mkdir -p circos/conf/ circos/data/ &&
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13
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14 #if $reference_genome.reference_genome_source == 'history':
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15 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
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16 #end if
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17
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18 #if $reference_genome.reference_genome_source != 'karyotype':
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19 ## Process the karyotype.txt file
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20 python '$__tool_directory__/fasta-to-karyotype.py'
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21
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22 #if str($reference_genome.reference_genome_source) == 'cached':
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23 '${reference_genome.fasta_indexes.fields.path}'
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24 #else if str($reference_genome.reference_genome_source) == 'history':
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25 genomeref.fa
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26 #end if
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27
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28 #if $reference_genome.bands:
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29 '${reference_genome.bands}'
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30 #end if
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31 > circos/conf/karyotype.txt &&
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32 #else
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33 cp $reference_genome.input_karyotype circos/conf/karyotype.txt &&
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34 #end if
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35
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36 mv '$circos_conf' circos/conf/circos.conf &&
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37 mv '$ticks_conf' circos/conf/ticks.conf &&
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38 mv '$ideogram_conf' circos/conf/ideogram.conf &&
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39 mv '$data_conf' circos/conf/2d.conf &&
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40 mv '$links_conf' circos/conf/links.conf &&
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41 mv '$test_case_conf' circos/conf/galaxy_test_case.xml &&
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42
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43 ## 2D Data Plots
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44 #for $hi, $data in enumerate($sec_tdd.data):
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45 #if str($data.plot_format.plot_format_select) == 'tile':
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46 python '$__tool_directory__/unified-tiles.py'
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47 '${data.plot_format.data_source}' '${data.plot_format.data_source.ext}'
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48 > circos/data/data-${hi}.txt &&
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49 #else:
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50 python $__tool_directory__/unified-histogram.py
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51 $data.plot_format.plot_format_select
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52 #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'):
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53 #for $fi, $file in enumerate($data.plot_format.data_source):
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54 '${file}' '${file.ext}'
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55 #end for
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56 #else:
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57 '${data.plot_format.data_source}' '${data.plot_format.data_source.ext}'
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58 #end if
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59 > circos/data/data-${hi}.txt &&
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60 #end if
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61 #end for
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62
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63 ## Link Tracks
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64 #for $hi, $data in enumerate($sec_links.data):
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65 cp '${data.data_source}' circos/data/links-${hi}.txt &&
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66 #end for
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67
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68 tar cvfz circos.tar.gz circos &&
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69
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70 circos -conf circos/conf/circos.conf
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71 ]]></command>
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72 <configfiles>
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73 <expand macro="configfile_circos_conf" />
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74 <expand macro="configfile_ticks_conf" />
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75 <expand macro="configfile_ideogram_conf" />
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76 <expand macro="configfile_data_conf" />
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77 <expand macro="configfile_links_conf" />
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78 <expand macro="test_case" />
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79 </configfiles>
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80 <inputs>
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81 <conditional name="reference_genome">
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82 <param name="reference_genome_source" type="select" label="Reference Genome">
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83 <option value="history" selected="True">From History</option>
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84 <option value="cached">Locally Cached</option>
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85 <option value="karyotype">Karyotype</option>
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86 </param>
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87 <when value="cached">
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88 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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89 <options from_data_table="all_fasta"/>
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90 </param>
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91 <!-- TODO: multiple band files? -->
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92 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
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93 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
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94 </when>
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95 <when value="history">
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96 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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97 <!-- TODO: multiple band files? -->
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98 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
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99 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
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100 </when>
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101 <when value="karyotype">
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102 <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration"/>
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103 </when>
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104 </conditional>
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105
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106 <section name="ideogram" title="Ideogram Configuration (Genome/Chromosomes)">
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107 <param name="spacing" type="float" value="0.005" label="Spacing Between Ideograms"/>
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108 <param name="radius" type="float" value="0.90" label="Radius"/>
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109 <param name="thickness" type="float" value="10" label="Thickness"/>
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110
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111 <section name="ideogram_labels" title="Labels">
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112 <param name="show_label" type="boolean" truevalue="yes" falsevalue="no" label="Show Label"/>
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113 <!--<param type="float" value="0.95" label="Radius" name="radius"/>-->
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114 <!--<param type="float" value="10" label="Thickness" name="thickness"/>-->
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115 <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no"
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116 help="When set to yes/true, labels will be perpendicular to the tangent of the circle at the location of the label. Otherwise, they will be parallel with the tangent of the circle"/>
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117 </section>
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118 </section>
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119
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120 <section name="ticks" title="Ticks">
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121 <param name="show_ticks" type="boolean" truevalue="yes" falsevalue="no" label="Show Ticks"/>
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122 <!--<param type="boolean" label="Show Tick Labels" name="show_tick_labels" truevalue="true" falsevalue="false" />-->
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123 <param name="radius" type="float" value="1.0" label="Radius"/>
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124 <expand macro="circos_color"/>
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125 <param name="multiplier" type="float" value="1e-3" label="Multiplier"
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126 help="1e-3 means your tick spacing will be in kb (tick spacing of 5000 = every 5kb, labels will read '5kb'). 1e-6 means mb."/>
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127
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128 <repeat name="tick_group" title="Tick Group">
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129 <param name="spacing" type="float" value="5000" label="Tick Spacing" help="Number of bases"/>
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130 <param name="size" type="float" value="10" label="Tick Size"/>
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131 <param name="show_tick_labels" type="boolean" truevalue="yes" falsevalue="no" label="Show Tick Labels"/>
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132 <param name="label_size" type="float" value="20" label="Label Size"/>
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133 <param name="label_offset" type="float" value="10" label="Label Offset"/>
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134 <param name="format" type="select" label="Label Format">
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135 <option value="%d" selected="True">Integer</option>
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136 <option value="%f">Float</option>
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137 <option value="%.1f">Float (one decimal)</option>
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138 <option value="%.2f">Float (two decimals)</option>
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139 <sanitizer>
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140 <valid>
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141 <add value="%" />
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142 </valid>
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143 </sanitizer>
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144 </param>
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145 </repeat>
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146
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147 </section>
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148
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149 <section name="sec_tdd" title="2D Data">
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150 <repeat name="data" title="2D Data Plot">
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151 <!-- Positioning -->
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152 <param name="r1" type="float" value="0.89" label="Outside Radius"/>
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153 <param name="r0" type="float" value="0.8" label="Inside Radius"/>
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154 <param name="orientation" type="boolean" label="Orient Inwards" truevalue="in" falsevalue="out"
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155 help="When yes/true, the plot will face inwards. I.e. lowest values will be to the outside"/>
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156
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157 <conditional name="plot_format">
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158 <param name="plot_format_select" type="select" label="Plot Format">
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159 <option value="histogram" selected="True">Histogram</option>
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160 <option value="heatmap">Heatmap</option>
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161 <option value="line">Line</option>
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162 <option value="scatter">Scatter</option>
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163 <option value="tile">Tiles</option>
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164 </param>
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165 <when value="histogram">
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166 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Histogram Data Source"
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167 multiple="True" help="If multiple files are selected, they will be treated as a stacked histogram"/>
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168 <section name="format_specific" title="Plot Format Specific Options">
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169 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
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170 <param name="extend_bins" type="boolean" label="Join non-abutting Bins" truevalue="yes" falsevalue="no"
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171 help="Join histogram bins that do not touch (abut)" />
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172 </section>
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173 </when>
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174 <when value="heatmap">
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175 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Heatmap Data Source"
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176 multiple="True" help="If multiple files are selected, they will be plotted alongside each other radially"/>
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177 <section name="format_specific" title="Plot Format Specific Options">
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178 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
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179 <param name="scale_log_base" type="float" value="1.0" label="Scale Log Base"
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180 help="If scale_log_base&lt;1, the dynamic range of color mapping of small values will be increased. If scale_log_base&gt;1, then dynamic range of large values will be increased."/>
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181 </section>
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182 </when>
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183 <when value="line">
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184 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Line Data Source"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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185 <section name="format_specific" title="Plot Format Specific Options">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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186 <expand macro="circos_color" label="Stroke Color" name="color" value="#000000"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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187 <param name="thickness" type="integer" value="0" label="Stroke Thickness"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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188 </section>
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189 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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190 <when value="scatter">
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191 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Scatter Plot Data Source"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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192 <section name="format_specific" title="Plot Format Specific Options">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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193 <!-- glyph, glyph_size, min, max -->
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194 <param name="glyph" type="select" label="Glyph">
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195 <option value="circle">Circle</option>
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196 <option value="triangle">Triangle</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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197 <option value="rectangle">Rectangle</option>
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198 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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199 <param name="glyph_size" type="integer" value="8" label="Glyph Size"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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200 <param name="data_min" type="float" value="0.0" label="Data Minimum" help="Minimum value of the range of the plot axis, data outside this range are clipped." />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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201 <param name="data_max" type="float" value="1.0" label="Data Maximum" help="Maximum value of the range of the plot axis, data outside this range are clipped." />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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202 <expand macro="circos_color" name="color" value="#555555" label="Color" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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203 <expand macro="circos_color" name="stroke_color" value="#000000" label="Stroke Color"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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204 <param name="stroke_thickness" type="integer" value="0" label="Stroke Thickness"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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205 </section>
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206 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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207 <when value="tile">
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208 <param name="data_source" type="data" format="bed6,bed12,gff3" label="Tile Data Source"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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209 help="If your tile source features have scores in them, they will be used in colouration"/>
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210 <section name="format_specific" title="Plot Format Specific Options">
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211 <expand macro="brewer_scale" name="fill_color" label="Fill Color"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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212 <expand macro="circos_color" name="color" value="#000000" label="Stroke Color"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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213 <param name="stroke_thickness" type="integer" value="0" label="Stroke Thickness"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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214 <param name="layers" type="integer" value="15" label="Layers"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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215 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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216 <param name="padding" type="float" value="8" label="Padding" help="In pixels"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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217
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218 <conditional name="overflow">
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219 <param name="overflow_behavior" type="select" label="Overflow Behavior">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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220 <option value="hide">Hide: overflow tiles are not drawn</option>
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221 <option value="grow">Grow: new layers are added as required</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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222 <option value="collapse">Collapse: overflow tiles are drawn on the first layer</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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223 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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224 <when value="hide">
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225 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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226 <when value="grow">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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227 <expand macro="circos_color" name="layer_overflow_color" label="Layer Overflow Color"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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228 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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229 <when value="collapse">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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230 <expand macro="circos_color" name="layer_overflow_color" label="Layer Overflow Color"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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231 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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232 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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233 </section>
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234 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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235 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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236
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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237 <expand macro="rules" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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238 <expand macro="axes" />
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239 <expand macro="backgrounds" />
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240 </repeat>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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241 </section>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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242 <section name="sec_links" title="Link Tracks">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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243 <repeat name="data" title="Link Data">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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244 <!-- Positioning -->
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245 <param name="radius" type="float" value="0.8" label="Inside Radius"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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246 help="This is the radial position of the termination of the link; for relative values, if radius smaller than 1 then it is defined in terms of the inner ideogram radius, otherwise it is defined in terms of the outer ideogram radius" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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247 <param name="data_source" type="data" format="txt" label="Link Data Source" help="Select file with link data. Format: chr1 start1 end1 chr2 start2 end2" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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248 <conditional name="linktype">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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249 <param name="ribbon" type="select" label="Link Type" help="">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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250 <option value="no" selected="true">basic</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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251 <option value="yes">ribbon</option>
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252 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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253 <when value="yes">
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254 <param name="twist" type="select" label="Twist Ribbon">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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255 <option value="" selected="true">auto</option>
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256 <option value="twist=yes">always</option>
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257 <option value="flat=yes">never</option>
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258 </param>
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259 </when>
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iuc
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260 <when value="no"/>
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261 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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262 <expand macro="circos_color" name="color" value="#000000" label="Link Color"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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263 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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264 <param name="bezier_radius" type="float" value="0.1" min="0" max="1" label="Bezier Radius"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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265 help="The radial position of the third control point (in addition to the two positions defined by the link coordinates) used to draw the Bezier curve; if this parameter is 0 then straight lines will be used"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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266
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267 <section name="advanced" title="Advanced Settings">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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268 <param name="zdepth" type="float" value="" optional="true" label="Z-depth"
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iuc
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269 help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple link tracks"/>
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270 <param name="crest" type="float" value="0.5" min="0" max="1" label="Crest"
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271 help="Two additional Bezier control points can be set by using the crest parameter. When defined, points p3 and p4 are added. These points lie at the same angular position as the start and end link termini and have the radial position. In the crest=0 extreme, p3 and p4 are at the same position as p0,p1. In this case, crest has no effect. When crest=1, p3,p4 are at the radial position of p2, the control point set by bezier_radius"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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272 <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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273 help="The bezier_radius_purity adjusts the position of p2 for each link. The p2 control point will move along the line formed by the original p2 location and the intersection of p0-p1 and the bisecting radius. When purity = 1, p2' = p2. When purity = 0, p2' = midpoint(p0,p1)"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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274 <conditional name="perturbation">
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275 <param name="perturb" type="select" label="Perturb links?"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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276 help="A set of parameters can be used to randomly adjust bezier_radius, bezier_radius_purity, and crest parameters to give the links a more disorganized, organic feel. By perturbing each link you can also show additional texture in the data among links which would have ordinarily overlapped. Each parameter's perturbation amount is defined as a pair of values - pmin,pmax. These are the minimum and maximum multipliers by which the value can be perturbed">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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277 <option value="no" selected="true">no</option>
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278 <option value="yes">yes</option>
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279 </param>
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280 <when value="yes">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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281 <param name="perturb_crest_min" type="float" value="0.5" label="Crest min"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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282 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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283 <param name="perturb_crest_max" type="float" value="1.5" label="Crest max"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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284 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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285 <param name="perturb_bezier_radius_min" type="float" value="0.5" label="Bezier Radius min"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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286 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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287 <param name="perturb_bezier_radius_max" type="float" value="1.5" label="Bezier Radius max"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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288 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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289 <param name="perturb_bezier_radius_purity_min" type="float" value="0.5" label="Bezier Radius Purity min"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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290 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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291 <param name="perturb_bezier_radius_purity_max" type="float" value="1.5" label="Bezier Radius Purity max"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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292 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
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293 </when>
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294 <when value="no"/>
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295 </conditional>
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296 </section>
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297 <expand macro="linkrules"/>
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298 </repeat>
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299 </section>
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300 </inputs>
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301 <outputs>
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302 <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot (png)"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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303 <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot (svg)"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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304 <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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305 </outputs>
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306 <tests>
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307 <test>
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308 <param name="reference_genome|reference_genome_source" value="history"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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309 <param name="reference_genome|genome_fasta" value="1/input.fa" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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310 <!-- ideograms -->
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311 <param name="ideogram|spacing" value="0.005" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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312 <param name="ideogram|radius" value="0.9" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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313 <param name="ideogram|thickness" value="10.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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314 <param name="ideogram|ideogram_labels|show_label" value="yes" />
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315 <param name="ideogram|ideogram_labels|parallel" value="no" />
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316 <!-- Ticks -->
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317 <param name="ticks|show_ticks" value="yes" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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318 <param name="ticks|radius" value="1.0" />
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319 <param name="ticks|color" value="#17365d" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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320 <param name="ticks|multiplier" value="0.001" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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321 <param name="ticks|tick_group_0|tickspacing" value="5000.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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322 <param name="ticks|tick_group_0|size" value="20.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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323 <param name="ticks|tick_group_0|show_tick_labels" value="yes" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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324 <param name="ticks|tick_group_0|label_size" value="20.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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325 <param name="ticks|tick_group_0|label_offset" value="10.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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326 <param name="ticks|tick_group_0|label_format" value="%d" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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327 <param name="ticks|tick_group_1|tickspacing" value="500.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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328 <param name="ticks|tick_group_1|size" value="10.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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329 <param name="ticks|tick_group_1|show_tick_labels" value="no" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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330 <param name="ticks|tick_group_1|label_size" value="20.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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331 <param name="ticks|tick_group_1|label_offset" value="10.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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332 <param name="ticks|tick_group_1|label_format" value="%d" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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333 <!-- Data -->
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334 <param name="sec_tdd|data_0|r0" value="0.8" />
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335 <param name="sec_tdd|data_0|r1" value="0.89" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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336 <param name="sec_tdd|data_0|orientation" value="out" />
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337 <param name="sec_tdd|data_0|plot_format|plot_format_select" value="histogram" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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338 <param name="sec_tdd|data_0|plot_format|data_source" value="1/0-0.wig" />
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339 <param name="sec_tdd|data_0|plot_format|format_specific|fill_color" value="purples-13-seq" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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340 <param name="sec_tdd|data_0|plot_format|format_specific|extend_bins" value="no" />
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341
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342 <param name="sec_tdd|data_1|r0" value="0.7" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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343 <param name="sec_tdd|data_1|r1" value="0.79" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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344 <param name="sec_tdd|data_1|orientation" value="out" />
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345 <param name="sec_tdd|data_1|plot_format|plot_format_select" value="tile" />
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346 <param name="sec_tdd|data_1|plot_format|data_source" value="1/1.gff3" />
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347 <param name="sec_tdd|data_1|plot_format|format_specific|fill_color" value="rdylgn-15-div" />
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348 <param name="sec_tdd|data_1|plot_format|format_specific|color" value="#000000" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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349 <param name="sec_tdd|data_1|plot_format|format_specific|stroke_thickness" value="1" />
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350 <param name="sec_tdd|data_1|plot_format|format_specific|layers" value="15" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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351 <param name="sec_tdd|data_1|plot_format|format_specific|thickness" value="15.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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352 <param name="sec_tdd|data_1|plot_format|format_specific|padding" value="8.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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353 <param name="sec_tdd|data_1|plot_format|format_specific|overflow|overflow_behavior" value="grow" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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354 <param name="sec_tdd|data_1|plot_format|format_specific|overflow|layer_overflow_color" value="#ffc000" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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355
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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356 <param name="sec_tdd|data_2|r0" value="0.6" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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357 <param name="sec_tdd|data_2|r1" value="0.69" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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358 <param name="sec_tdd|data_2|orientation" value="out" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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359 <param name="sec_tdd|data_2|plot_format|plot_format_select" value="scatter" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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360 <param name="sec_tdd|data_2|plot_format|data_source" value="1/2.wig" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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361 <param name="sec_tdd|data_2|plot_format|format_specific|glyph" value="triangle" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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362 <param name="sec_tdd|data_2|plot_format|format_specific|glyph_size" value="8" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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363 <param name="sec_tdd|data_2|plot_format|format_specific|data_min" value="0.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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364 <param name="sec_tdd|data_2|plot_format|format_specific|data_max" value="1.0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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365 <param name="sec_tdd|data_2|plot_format|format_specific|color" value="#555555" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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366 <param name="sec_tdd|data_2|plot_format|format_specific|stroke_color" value="#000000" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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367 <param name="sec_tdd|data_2|plot_format|format_specific|stroke_thickness" value="0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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368 <!-- Links -->
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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369 <param name="sec_links|data_0|radius" value="0.59" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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370 <param name="sec_links|data_0|data_source" value="1/links.txt" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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371 <param name="sec_links|data_0|linktype|ribbon" value="yes" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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372 <param name="sec_links|data_0|color" value="#9966ff" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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373 <param name="sec_links|data_0|bezier_radius" value="0.3" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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374 <param name="sec_links|data_0|sec_link_rule|rules_0|conditions_0|application|application_select" value="pos1" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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375 <param name="sec_links|data_0|sec_link_rule|rules_0|conditions_0|application|comparison|compare" value="lt" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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376 <param name="sec_links|data_0|sec_link_rule|rules_0|conditions_0|application|comparison|compval" value="25000" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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377 <param name="sec_links|data_0|sec_link_rule|rules_0|actions_0|action|action_select" value="color" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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378 <param name="sec_links|data_0|sec_link_rule|rules_0|actions_0|action|action_value" value="#ffcc00" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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379
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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380 <param name="sec_links|data_1|radius" value="0.45" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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381 <param name="sec_links|data_1|data_source" value="1/links2.txt" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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382 <param name="sec_links|data_1|linktype|ribbon" value="yes" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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383 <param name="sec_links|data_1|color" value="#42aa42" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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384 <param name="sec_links|data_1|bezier_radius" value="0" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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385
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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386 <!-- Outputs -->
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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387 <output name="output_png" file="1/output.png" compare="sim_size" delta="15000" ftype="png" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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388 <output name="output_svg" file="1/output.svg" compare="sim_size" ftype="svg" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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389 </test>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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390 </tests>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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391 <help><![CDATA[
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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392 Circos
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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393 ======
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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394
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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395 Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive.
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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396
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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397 Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience.
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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398
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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399 .. image:: $PATH_TO_IMAGES/circos-sample-panel.png
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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400 :alt: several example circos plots
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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401
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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402 For more information see the Circos documentation_.
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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403
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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404 .. _documentation: http://circos.ca/documentation/
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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405
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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406
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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407 ]]></help>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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408 <expand macro="citations" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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409 </tool>