annotate circos.xml @ 3:fd59d783248a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f04fe62fb7dbad75e597da8cd674cfe36ed3d80a"
author iuc
date Mon, 02 Dec 2019 08:14:29 -0500
parents 014a21767ac4
children 184dfd9e113d
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014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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1 <?xml version="1.0"?>
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2 <tool id="circos" name="Circos" version="@WRAPPER_VERSION@">
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3 <description>visualizes data in a circular layout</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 <import>macros_tests.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <version_command>circos --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ## Directory structure
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13 mkdir -p circos/conf/ circos/data/ &&
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14
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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15 #if $reference_genome.ref.ref_source == 'history':
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16 ln -s '$reference_genome.ref.genome_fasta' genomeref.fa &&
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17 #end if
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18
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19 #if $reference_genome.ref.ref_source in ('lengths', 'cached'):
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20 python '$__tool_directory__/genome-lengths-to-karyotype.py'
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21 #if $reference_genome.ref.ref_source == 'lengths':
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22 ${reference_genome.ref.input_lengths}'
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23 #else
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24 #if $ideogram.limit_chromosomes:
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25 ## If they are limiting the chromosomes, ensure they have access to the full list
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26 '${reference_genome.ref.fasta_indexes.fields.len_path}'
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27 #else
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28 ## Otherwise only the reduced list, as the full list will often overwhelm circos
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29 <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}')
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30 #end if
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31 #end if
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32 '${ideogram.color}'
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33 > circos/conf/karyotype.txt &&
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34 #else if $reference_genome.ref.ref_source == 'karyotype':
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35 cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt &&
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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36 #else if str($reference_genome.ref.ref_source) == 'history':
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37 ## Process the karyotype.txt file
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38 python
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39 '$__tool_directory__/fasta-to-karyotype.py'
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40 genomeref.fa
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41 '${ideogram.color}'
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42
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43 > circos/conf/karyotype.txt &&
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44 #end if
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45
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46 touch circos/conf/karyotype-colors.conf &&
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47 #if $ideogram.bands.bands:
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48 #if $ideogram.bands.convert_bands:
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49 python '$__tool_directory__/process-cytogenetic-bands.py'
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50 '${ideogram.bands.bands}'
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51 >> circos/conf/karyotype.txt
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52 2> circos/conf/karyotype-colors.conf &&
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53 #else
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54 cat '${ideogram.bands.bands}'
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55 >> circos/conf/karyotype.txt &&
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56 #end if
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57 #end if
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58
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59 #if $plot_options.colour_profile:
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60 #if str($plot_options.colour_profile) == 'cg':
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61 cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf &&
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62 #end if
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63 #end if
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64
3
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65 cp '$circos_conf' circos/conf/circos.conf &&
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66 cp '$ticks_conf' circos/conf/ticks.conf &&
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67 cp '$ideogram_conf' circos/conf/ideogram.conf &&
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68 cp '$data_conf' circos/conf/data.conf &&
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69 cp '$highlight_conf' circos/conf/highlight.conf &&
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70 cp '$links_conf' circos/conf/links.conf &&
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71 cp '$test_case_conf' circos/conf/galaxy_test_case.json &&
2
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72
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73 ## Highlights
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74 #for $hi, $data in enumerate($sec_highlight.data):
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75 cp '${data.data_source}' circos/data/highlight-${hi}.txt &&
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76 #end for
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77
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78 ## 2D Data Plots
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79 #for $hi, $data in enumerate($sec_tdd.data):
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80 cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt &&
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81 #end for
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82
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83 ## Link Tracks
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84 #for $hi, $data in enumerate($sec_links.data):
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85 cp '${data.data_source}' circos/data/links-${hi}.txt &&
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86 #end for
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87
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88 #if $outputs.tar == "yes"
3
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89 tar -czf circos.tar.gz circos &&
2
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90 #end if
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91
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92 #if $outputs.svg == "yes" or $outputs.png == "yes":
3
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93 circos -conf circos/conf/circos.conf -noparanoid
2
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94 #end if
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95 ]]></command>
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96 <configfiles>
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97 <expand macro="configfile_circos_conf" />
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98 <expand macro="configfile_ticks_conf" />
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99 <expand macro="configfile_ideogram_conf" />
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100 <expand macro="configfile_data_conf" />
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101 <expand macro="configfile_links_conf" />
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102 <expand macro="configfile_highlight_conf" />
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103 <expand macro="test_case" />
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104 </configfiles>
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105 <inputs>
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106 <section name="reference_genome" title="Karyotype" expanded="true">
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107 <conditional name="ref">
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108 <param name="ref_source" type="select" label="Reference Genome Source">
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109 <option value="history" selected="True">FASTA File from History</option>
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110 <option value="cached">Locally Cached</option>
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111 <option value="karyotype">Karyotype</option>
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112 <option value="lengths">Lengths File</option>
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113 </param>
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114 <!--
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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115 This does not work at all for us. Many dbkeys lengths simply have too many contigs that are completely irrelevant for 99% of plotting operations. Our options were:
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116
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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117 - picking for the user (will never be right)
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118 - picking some N contigs (also never right)
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119 - regex (eww, and requires users to know thje names of things in the data table which is not exposed to user ever.)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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120 - built in custom filters we'd have to maintain
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121 - some code files (see meme_chip.xml, doesn't work there.)
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122
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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123 - using one of the legacy chromosomes that doesn't include detritus
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124
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125 But none of the optinos work well or uniformly, so, no. We're forced to remove this as an option completely.
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126
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127 -->
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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128 <when value="cached">
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129 <param name="fasta_indexes" type="select" label="Source Genome Build" help="Warning: this also contains unplaced scaffolds present in the reference genome. You can restrict the regions to plot in 'Limit/Filter Chromosomes' below, or supply your own file.">
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130 <options from_data_table="__dbkeys__"/>
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131 </param>
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132 </when>
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133 <when value="history">
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134 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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135 </when>
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136 <when value="karyotype">
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137 <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration" help="Provide your own karyotype configuration. Should be 'chr - ID LABEL START END COLOR'"/>
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138 </when>
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139 <when value="lengths">
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140 <param name="input_lengths" type="data" format="tabular" label="Sequence Lengths" help="This needs to be a 2+ column tabular, e.g. from 'Compute sequence lengths', the first column should be chromosome and second should be length."/>
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141 </when>
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142 </conditional>
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143 </section>
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144
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145 <section name="sec_tdd" title="2D Data Tracks">
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146 <repeat name="data" title="2D Data Plot" help="2D Data Plots allow you to graph all sorts of data visually such as scatter or line plots, heatmaps, or tiles representing gene locations. These are commonly used to plot sequencing density tracks or other datasets that have some value at different positions along a genome.">
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147 <!-- Positioning -->
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148 <param name="r1" type="float" value="0.89" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/>
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149 <param name="r0" type="float" value="0.8" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/>
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150
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151
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152 <conditional name="plot_format">
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153 <param name="plot_format_select" type="select" label="Plot Type">
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154 <option value="histogram" selected="True">Histogram</option>
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155 <option value="histogram-stacked">Stacked Histogram</option>
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156 <option value="heatmap">Heatmap</option>
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157 <option value="line">Line</option>
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158 <option value="scatter">Scatter</option>
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159 <option value="tile">Tiles</option>
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160 <option value="text">Text Labels</option>
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161 </param>
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162 <when value="histogram">
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163 <param name="data_source" type="data" format="tabular,interval" label="Histogram Data Source" help="Columns must be (chrom, start, end, value)"/>
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164 <section name="format_specific" title="Plot Format Specific Options">
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165 <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#ffdcfc"/>
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166 <expand macro="stroke_opts"/>
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167
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168 <param name="fill_under" type="boolean" label="Fill underneath the histogram" truevalue="yes" falsevalue="no" checked="true" />
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169 <param name="extend_bins" type="boolean" label="Join non-abutting Bins" truevalue="yes" falsevalue="no"
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170 help="Join histogram bins that do not touch (abut)" />
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171 </section>
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172 </when>
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173 <when value="histogram-stacked">
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174 <param name="data_source" type="data" format="tabular,interval" label="Histogram Data Source" help="Columns must be (chrom, start, end, values). Values should be comma-separated"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
175 <section name="format_specific" title="Plot Format Specific Options">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
176 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
177 <expand macro="stroke_opts"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
178
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
179 <param name="fill_under" type="boolean" label="Fill underneath the histogram" truevalue="yes" falsevalue="no" checked="true" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
180 <param name="extend_bins" type="boolean" label="Join non-abutting Bins" truevalue="yes" falsevalue="no"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
181 help="Join histogram bins that do not touch (abut)" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
182
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
183 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
184 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
185 <when value="heatmap">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
186 <param name="data_source" type="data" format="tabular,interval" label="Heatmap Data Source" help="Columns must be (chrom, start, end, value)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
187 <section name="format_specific" title="Plot Format Specific Options">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
188 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
189 <param name="scale_log_base" type="float" value="1.0" label="Scale Log Base"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
190 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."/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
191 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
192 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
193 <when value="line">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
194 <param name="data_source" type="data" format="tabular,interval" label="Line Data Source" help="Columns must be (chrom, start, end, value)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
195 <section name="format_specific" title="Plot Format Specific Options">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
196 <expand macro="stroke_opts"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
197 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
198 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
199 <when value="scatter">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
200 <param name="data_source" type="data" format="tabular,interval" label="Scatter Plot Data Source" help="Columns must be (chrom, start, end, value)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
201 <section name="format_specific" title="Plot Format Specific Options">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
202 <!-- glyph, glyph_size, min, max -->
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
203 <param name="glyph" type="select" label="Glyph">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
204 <option value="circle">Circle</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
205 <option value="triangle">Triangle</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
206 <option value="rectangle">Rectangle</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
207 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
208 <param name="glyph_size" type="integer" value="8" label="Glyph Size"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
209 <expand macro="circos_color_alpha" name="fill_color" value="#555555" label="Color" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
210 <expand macro="stroke_opts"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
211 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
212 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
213 <when value="tile">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
214 <param name="data_source" type="data" format="tabular,interval" label="Tile Data Source"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
215 help="Column must be (chrom, start, end)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
216 <section name="format_specific" title="Plot Format Specific Options">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
217 <expand macro="circos_color_alpha" name="fill_color" label="Fill Color"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
218
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
219 <expand macro="stroke_opts"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
220 <param name="layers" type="integer" value="15" label="Layers"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
221 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
222 <param name="padding" type="float" value="8" label="Padding" help="In pixels"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
223 <param name="margin" type="float" value="0.002" label="Margin" help="In chromosome units. This is essentially distance added to the gene, before laying it out. Increasing it will prevent genes from packing as well."/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
224
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
225 <conditional name="overflow">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
226 <param name="overflow_behavior" type="select" label="Overflow Behavior">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
227 <option value="hide">Hide: overflow tiles are not drawn</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
228 <option value="grow">Grow: new layers are added as required</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
229 <option value="collapse">Collapse: overflow tiles are drawn on the first layer</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
230 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
231 <when value="hide">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
232 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
233 <when value="grow">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
234 <expand macro="circos_color" name="layer_overflow_color" label="Layer Overflow Color"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
235 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
236 <when value="collapse">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
237 <expand macro="circos_color" name="layer_overflow_color" label="Layer Overflow Color"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
238 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
239 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
240 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
241 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
242 <when value="text">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
243 <param name="data_source" type="data" format="tabular,interval" label="Text Data Source" help="Columns must be (chrom, start, end, text)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
244
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
245 <section name="format_specific" title="Plot Format Specific Options">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
246 <param name="label_size" type="integer" value="24" label="Label Size" min="1"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
247 <conditional name="link">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
248 <param name="show_link" type="select" label="Show Link">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
249 <option value="yes" selected="true">Yes</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
250 <option value="no">No</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
251 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
252 <when value="yes">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
253 <param name="link_thickness" type="integer" value="2" label="Link thickness" min="0" help="In pixels"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
254 <expand macro="circos_color" name="link_color" label="Link Color" value="#ff0000"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
255 <param name="link_dims" type="text" value="1p,2p,3p,2p,1p" label="Link dimensions">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
256 <sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
257 <valid initial="string.digits">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
258 <add value="p"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
259 <add value=","/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
260 </valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
261 </sanitizer>
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262 </param>
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263
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264 </when>
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265 <when value="no">
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266 </when>
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267 </conditional>
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268 <conditional name="snuggle">
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269 <param name="label_snuggle" type="select" label="Snuggle Labels" help="The label's radial position may be slightly adjusted to reduce the number of layers of text">
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270 <option value="yes">Yes</option>
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parents:
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271 <option value="no" selected="true">No</option>
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272 </param>
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parents:
diff changeset
273 <when value="yes">
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274 <param name="max_snuggle_distance" type="integer" value="2" min="0" label="Max snuggle Distance" help="Shift label up to N times its height, in the angular direction"/>
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275 <param name="snuggle_sampling" type="integer" value="2" min="1" label="Snuggle Sampling" help="Sample possible positions every N pixels"/>
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276 <param name="snuggle_tolerance" type="float" value="0.25" min="0" label="Snuggle Tolerance" help="You can also short-circuit precise placement by setting snuggle_tolerance (absolute or relative to label's tangential size). The larger this value, the less precise the placement. (from Circos manual)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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277 <param name="snuggle_link_overlap_test" type="boolean" truevalue="yes" falsevalue="no" checked="yes" label="Snuggle Link Overlap Test" help="If the labels have a link line, you choose to test whether link lines overlap with previous labels using snuggle_link_overlap_test (from Circos manual)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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278 <param name="snuggle_link_overlap_tolerance" type="float" value="2" min="0" label="Snuggle Link Overlap Tolerance" help="The extent of acceptable overlap is set using snuggle_link_overlap_tolerance (from Circos manual)"/>
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iuc
parents:
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279 <param name="snuggle_refine" type="boolean" truevalue="yes" falsevalue="no" checked="yes" label="Snuggle refine" help="The snuggle_refine parameter toggles an additional check for crossing of links of labels that are placed at similar radial positions. Label pairs whose link lines cross are swapped. This refine parameter is functionaly only if show_links=yes. (from Circos manual)"/>
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parents:
diff changeset
280 </when>
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iuc
parents:
diff changeset
281 <when value="no">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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parents:
diff changeset
282 </when>
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283 </conditional>
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284
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
285 </section>
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parents:
diff changeset
286 </when>
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diff changeset
287 </conditional>
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288 <param name="orientation" type="boolean" label="Orient Inwards" truevalue="in" falsevalue="out"
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diff changeset
289 help="When yes, the plot will face inwards; i.e. lowest values will be plotted to the outside"/>
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iuc
parents:
diff changeset
290 <expand macro="minmax" />
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parents:
diff changeset
291
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
292 <expand macro="rules" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
293 <expand macro="axes" />
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iuc
parents:
diff changeset
294 <expand macro="backgrounds" />
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parents:
diff changeset
295 </repeat>
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diff changeset
296 </section>
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iuc
parents:
diff changeset
297 <section name="sec_links" title="Link Tracks">
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parents:
diff changeset
298 <repeat name="data" title="Link Data" help="Link tracks show a relationship between two locations in your plot. They are often used for indicating sequence similarity between two regions of a genome, or some interaction between two groups.">
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diff changeset
299 <!-- Positioning -->
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300 <param name="radius" type="float" value="0.8" min="0" max="1" label="Inside Radius"
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diff changeset
301 help="This is the radial position of the termination of the link. Value must be between 1 (outer edge of plot) and 0 (center of the plot)" />
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302 <param name="data_source" type="data" format="tabular,interval" label="Link Data Source" help="Select file with link data. Format: chr1 start1 end1 chr2 start2 end2" />
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303 <conditional name="linktype">
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iuc
parents:
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304 <param name="ribbon" type="select" label="Link Type" help="">
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305 <option value="no">basic</option>
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306 <option value="yes" selected="true">ribbon</option>
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307 </param>
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diff changeset
308 <when value="yes">
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309 <param name="twist" type="select" label="Twist Ribbon" help="Fine grained control for display behaviour of ribbons">
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310 <option value="" selected="true">auto</option>
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311 <option value="twist=yes">always (twist)</option>
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312 <option value="flat=yes">never (flat)</option>
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diff changeset
313 </param>
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diff changeset
314 <param name="pattern" type="select" label="Ribbon background pattern">
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315 <option value="solid" selected="true">Solid</option>
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316 <option value="hline">Horizontal Lines</option>
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317 <option value="hline-sparse">Horizontal Lines (sparse)</option>
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parents:
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318 <option value="vline">Vertical Lines</option>
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parents:
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319 <option value="vline-sparse">Vertical Lines (sparse)</option>
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iuc
parents:
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320 <option value="checker">Checker</option>
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parents:
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321 <option value="checker-sparse">Checker (sparse)</option>
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iuc
parents:
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322 <option value="dot">Dots</option>
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iuc
parents:
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323 <option value="dot-sparse">Dots (sparse)</option>
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diff changeset
324 </param>
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diff changeset
325 </when>
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iuc
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diff changeset
326 <when value="no"/>
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327 </conditional>
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328 <expand macro="circos_color_alpha" name="color" value="#000000" label="Link Color"/>
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329 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/>
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330 <param name="bezier_radius" type="float" value="0.1" min="0" max="1" label="Bezier Radius"
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331 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"/>
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iuc
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332
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iuc
parents:
diff changeset
333 <section name="advanced" title="Advanced Settings">
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iuc
parents:
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334 <param name="zdepth" type="float" value="" optional="true" label="Z-depth"
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parents:
diff changeset
335 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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parents:
diff changeset
336 <param name="crest" type="float" value="0.5" min="0" max="1" label="Crest"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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337 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"/>
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diff changeset
338 <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity"
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diff changeset
339 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)"/>
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iuc
parents:
diff changeset
340 <conditional name="perturbation">
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iuc
parents:
diff changeset
341 <param name="perturb" type="select" label="Perturb links?"
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iuc
parents:
diff changeset
342 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">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
343 <option value="no" selected="true">no</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
344 <option value="yes">yes</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
345 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
346 <when value="yes">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
347 <param name="perturb_crest_min" type="float" value="0.5" label="Crest min"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
348 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
349 <param name="perturb_crest_max" type="float" value="1.5" label="Crest max"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
350 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
351 <param name="perturb_bezier_radius_min" type="float" value="0.5" label="Bezier Radius min"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
352 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
353 <param name="perturb_bezier_radius_max" type="float" value="1.5" label="Bezier Radius max"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
354 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
355 <param name="perturb_bezier_radius_purity_min" type="float" value="0.5" label="Bezier Radius Purity min"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
356 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
357 <param name="perturb_bezier_radius_purity_max" type="float" value="1.5" label="Bezier Radius Purity max"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
358 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
359 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
360 <when value="no"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
361 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
362 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
363 <expand macro="linkrules"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
364 </repeat>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
365 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
366
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
367 <section name="plot_options" title="General">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
368 <conditional name="background">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
369 <param name="background_select" type="select" label="Plot Background">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
370 <option value="transparent">Transparent</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
371 <option value="color" selected="true">Solid Color</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
372 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
373 <when value="transparent" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
374 <when value="color">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
375 <expand macro="circos_color" label="Background Color" name="background_color" value="#ffffff"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
376 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
377 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
378 <param name="radius" type="integer" label="Image Radius" value="1500" min="500" max="5000" help="Plot radius (in pixels), final plot dimensions will be 2*r by 2*r"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
379 <param name="colour_profile" type="select" label="Load additional colour profiles" optional="true" help="Only useful in a tiny subset of situations">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
380 <option value="cg">Complete Genomics</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
381 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
382 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
383
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
384 <section name="ideogram" title="Ideogram">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
385 <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="Note, this will be ignored if you supplied a karyogram file containing colour specifications"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
386 <param name="limit_chromosomes" type="text" optional="true" label="Limit/Filter Chromosomes" help="For example: 'hs1;hs2;hs3' or 'chr1:1-1000;chr2:3000-9000' to plot only a subset of regions">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
387 <sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
388 <valid initial="string.letters,string.digits">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
389 <add value=","/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
390 <add value="_"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
391 <add value="."/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
392 <add value=":"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
393 <add value=";"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
394 <add value="-"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
395 </valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
396 </sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
397 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
398 <param name="chromosomes_reverse" type="text" optional="true" label="Reverse these Chromosomes" help="Important: If you set this, you will need to set the 'Limit/Filter Chromosomes' option (above) as well">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
399 <sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
400 <valid initial="string.letters,string.digits">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
401 <add value=","/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
402 <add value="_"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
403 <add value="."/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
404 <add value=":"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
405 <add value=";"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
406 <add value="-"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
407 </valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
408 </sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
409 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
410
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
411 <param name="units" type="select" label="Chromosome units" help="Setting this to MB allows usage of numbers like 5u to represent 5MB, rather than having to specify 5000000 or 5e6">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
412 <option value="bases">Bases</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
413 <option value="kb">Kilobases</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
414 <option value="mb" selected="true">Megabases</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
415 <option value="gb">Gigabases</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
416 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
417
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
418 <param name="spacing" type="float" value="0.005" label="Spacing Between Ideograms" min="0"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
419 <param name="radius" type="float" value="0.90" label="Radius" min="0"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
420 <param name="thickness" type="float" value="10" label="Thickness" min="0"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
421
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
422 <section name="ideogram_labels" title="Labels">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
423 <param name="show_label" type="boolean" truevalue="yes" falsevalue="no" label="Show Label" checked="true"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
424 <param type="float" value="0.075" label="Radius" name="radius_offset"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
425 <param type="integer" value="24" label="Label Font Size" name="size"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
426 <!--<param type="float" value="10" label="Thickness" name="thickness"/>-->
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
427 <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no" checked="true"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
428 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"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
429 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
430
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
431 <section name="bands" title="Cytogenic Bands">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
432 <param name="bands" type="data" format="tabular" optional="true" label="Cytogenetic Bands"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
433 help="If defined, will display cytogenetic bands as part of the karyotype configuration. This field accepts any tabular format file. If you provide a BED file you should enable automatic conversion below. Otherwise disable conversion below and it is expected that your file have 7 columns: 'band', chromosome ID (should match fasta), band ID, band ID (again), start, end, color (gneg, gpos, or r,g,b triple). E.g. a complete row would look like: 'band chr1 p32.2 p32.2 56100000 59000000 gneg25'"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
434 <param name="convert_bands" type="boolean" truevalue="yes" falsevalue="no" label="Convert bands from BED format to circos karyotype band format" checked="true"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
435 help="Automatically reformat BED file into the appropriate columns. This should be a BED 6+ file, BED 9+ if you want the colours from the BED file automatically used. Otherwise everything will appear grey."/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
436 <param name="fill_bands" type="boolean" truevalue="yes" falsevalue="no" label="Fill Bands" checked="true"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
437 <param name="band_transparency" type="integer" label="Fill Bands" value="0" min="0" max="5" help="0 is solid, 1 is the least transparent, and 5 is the most transparent"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
438
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
439 <param type="integer" value="2" label="Band Stroke Thickness" name="band_stroke_thickness"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
440 <expand macro="circos_color" label="Band Stroke Color" name="band_stroke_color" value="#000000"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
441 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
442 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
443
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
444 <section name="ticks" title="Ticks">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
445 <param name="show_ticks" type="boolean" truevalue="yes" falsevalue="no" label="Show Ticks"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
446 <param name="radius" type="float" value="1.0" label="Radius"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
447 <param name="skip_first_label" type="boolean" truevalue="yes" falsevalue="no" label="Skip first label"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
448 <param name="skip_last_label" type="boolean" truevalue="yes" falsevalue="no" label="Skip last label"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
449
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
450 <repeat name="tick_group" title="Tick Group">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
451 <param name="spacing" type="text" value="5000" label="Tick Spacing" help="Number of bases (number + u syntax works)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
452 <param name="size" type="float" value="10" label="Tick Size"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
453 <expand macro="circos_color"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
454 <conditional name="ticks">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
455 <param name="show_tick_labels" type="select" label="Show Tick Labels">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
456 <option value="yes">Yes</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
457 <option value="no" selected="true">No</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
458 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
459 <when value="yes">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
460 <param name="label_size" type="float" value="20" label="Label Size"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
461 <param name="label_offset" type="float" value="10" label="Label Offset"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
462 <param name="format" type="select" label="Label Format">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
463 <option value="%d" selected="True">Integer</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
464 <option value="%f">Float</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
465 <option value="%.1f">Float (one decimal)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
466 <option value="%.2f">Float (two decimals)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
467 <sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
468 <valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
469 <add value="%" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
470 </valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
471 </sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
472 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
473 <param name="format_ext" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Show unit in tick labels" help="If your chromosome units is set to kilobases and you have enabled this option and enabled tick labels, they will include the size value, e.g. '500 kb' "/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
474 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
475 <when value="no">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
476 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
477 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
478 </repeat>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
479
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
480 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
481
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
482 <section name="sec_highlight" title="Highlights">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
483 <repeat name="data" title="Highlight" help="Highlights can help highlight a specific region by placing a large coloured block under some interesting or important features that the audience's eyes should be drawn towards">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
484 <param name="r1" type="float" value="0.89" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
485 <param name="r0" type="float" value="0.8" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
486 <param name="data_source" type="data" format="tabular,interval" label="Highlight Data Source" help="Columns must be (chrom, start, end)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
487 <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#000000"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
488 <expand macro="rules" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
489 </repeat>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
490 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
491
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
492 <section name="outputs" title="Outputs">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
493 <param name="png" type="boolean" truevalue="yes" falsevalue="no" label="PNG" checked="true"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
494 <param name="svg" type="boolean" truevalue="yes" falsevalue="no" label="SVG" checked="false" help="Oftentimes this will not be viewable directly in Galaxy, you may need to download this file first."/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
495 <param name="tar" type="boolean" truevalue="yes" falsevalue="no" label="Configuration Archive" checked="false" help="This contains all the files needed to make this plot. With the data contained within here, and a copy of Circos installed locally, you can rebuild the plot and make any manual changes that are not possible in Galaxy (e.g. colours not in the colour picker)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
496 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
497 </inputs>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
498 <outputs>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
499 <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
500 <filter>outputs['png']</filter>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
501 </data>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
502 <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
503 <filter>outputs['svg']</filter>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
504 </data>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
505 <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
506 <filter>outputs['tar']</filter>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
507 </data>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
508 </outputs>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
509 <expand macro="test_cases" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
510 <help><![CDATA[
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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511 Circos
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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512 ======
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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513
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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514 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.
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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515
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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516 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.
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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517
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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518 .. image:: $PATH_TO_IMAGES/circos-sample-panel.png
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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519 :alt: several example circos plots
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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520
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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521 For more information see the Circos documentation_.
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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522
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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523 .. _documentation: http://circos.ca/documentation/
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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524
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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525
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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526 ]]></help>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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527 <expand macro="citations" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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528 </tool>