Mercurial > repos > iuc > circos

annotate circos.xml @ 7:4b519282a05b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
author iuc
date Mon, 25 May 2020 10:52:02 -0400
parents 740057a5126d
children df7356989ac1
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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 <xrefs>
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5 <xref type="bio.tools">galactic_circos</xref>
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6 <!--<xref type="bioconda">circos</xref>-->
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7 <!--<xref type="rrid">RRID:SCR_018207</xref>-->
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8 </xrefs>
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9 <macros>
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10 <import>macros.xml</import>
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11 <import>macros_conffiles.xml</import>
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12 <import>macros_tests.xml</import>
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13 </macros>
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14 <expand macro="requirements"/>
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15 <version_command>circos --version</version_command>
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16 <stdio>
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17 <!-- Anything other than zero is an error -->
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18 <exit_code range="1:"/>
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19 <exit_code range=":-1"/>
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20 <!-- In case the return code has not been set propery check stderr too -->
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21 <regex match="Circos::Error::fatal_error.* called at"/>
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22 </stdio>
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23 <command><![CDATA[
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24 ## Directory structure
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25 mkdir -p circos/conf/ circos/data/ &&
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26
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27 #if $reference_genome.ref.ref_source == 'history':
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28 ln -s '$reference_genome.ref.genome_fasta' genomeref.fa &&
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29 #end if
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31 #if $reference_genome.ref.ref_source in ('lengths', 'cached'):
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32 python '$__tool_directory__/karyotype-from-lengths.py'
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33 #if $reference_genome.ref.ref_source == 'lengths':
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34 ${reference_genome.ref.input_lengths}'
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35 #else
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36 #if $ideogram.limit_chromosomes:
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37 ## If they are limiting the chromosomes, ensure they have access to the full list
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38 '${reference_genome.ref.fasta_indexes.fields.len_path}'
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39 #else
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40 ## Otherwise only the reduced list, as the full list will often overwhelm circos
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41 <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}')
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42 #end if
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43 #end if
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44 > circos/conf/karyotype.txt &&
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45 #else if $reference_genome.ref.ref_source == 'karyotype':
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46 cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt &&
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47 #else if str($reference_genome.ref.ref_source) == 'history':
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48 ## Process the karyotype.txt file
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49 python
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50 '$__tool_directory__/karyotype-from-fasta.py'
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51 genomeref.fa
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52 > circos/conf/karyotype.txt &&
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53 #else if $reference_genome.ref.ref_source == 'preset':
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54 cp '$__tool_directory__/karyotype/'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt &&
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55 #end if
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56
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57 python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'`
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58 > 'circos/conf/karyotype-colors.conf' &&
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59
2
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60 touch circos/conf/karyotype-colors.conf &&
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61
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62 ## #if $ideogram.bands.bands:
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63 ## #if $ideogram.bands.convert_bands:
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64 ## python '$__tool_directory__/process-cytogenetic-bands.py'
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65 ## '${ideogram.bands.bands}'
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66 ## >> circos/conf/karyotype.txt
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67 ## 2> circos/conf/karyotype-colors.conf &&
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68 ## #else
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69 ## cat '${ideogram.bands.bands}'
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70 ## >> circos/conf/karyotype.txt &&
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71 ## #end if
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72 ## #end if
2
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73
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74 #if $plot_options.colour_profile:
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75 #if str($plot_options.colour_profile) == 'cg':
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76 cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf &&
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77 #end if
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78 #end if
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79
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80 cp '$circos_conf' circos/conf/circos.conf &&
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81 cp '$ticks_conf' circos/conf/ticks.conf &&
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82 cp '$ideogram_conf' circos/conf/ideogram.conf &&
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83 cp '$data_conf' circos/conf/data.conf &&
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84 cp '$links_conf' circos/conf/links.conf &&
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85 cp '$test_case_conf' circos/conf/galaxy_test_case.json &&
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86
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87 ## 2D Data Plots
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88 #for $hi, $data in enumerate($sec_tdd.data):
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89 cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt &&
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90 #end for
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91
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92 ## Link Tracks
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93 #for $hi, $data in enumerate($sec_links.data):
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94 cp '${data.data_source}' circos/data/links-${hi}.txt &&
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95 #end for
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96
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97 #if $outputs.tar == "yes"
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98 tar -czf circos.tar.gz circos &&
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99 #end if
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100
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101 #if $outputs.svg == "yes" or $outputs.png == "yes":
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102 circos -conf circos/conf/circos.conf -noparanoid
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103 #end if
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104 ]]></command>
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105 <configfiles>
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106 <expand macro="configfile_circos_conf" />
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107 <expand macro="configfile_ticks_conf" />
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108 <expand macro="configfile_ideogram_conf" />
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109 <expand macro="configfile_data_conf" />
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110 <expand macro="configfile_links_conf" />
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111 <expand macro="test_case" />
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112 </configfiles>
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113 <inputs>
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114 <section name="reference_genome" title="Karyotype" expanded="true">
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115 <conditional name="ref">
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116 <param name="ref_source" type="select" label="Reference Genome Source">
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117 <option value="preset" selected="True">Circos Presets</option>
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118 <option value="history"> FASTA File from History (can be slow, generate a length file to improve execution time.)</option>
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119 <option value="cached">Locally Cached</option>
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120 <option value="karyotype">Custom Karyotype</option>
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121 <option value="lengths">Lengths File</option>
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122 </param>
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123 <!--
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124 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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125
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126 - picking for the user (will never be right)
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127 - picking some N contigs (also never right)
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128 - regex (eww, and requires users to know thje names of things in the data table which is not exposed to user ever.)
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129 - built in custom filters we'd have to maintain
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130 - some code files (see meme_chip.xml, doesn't work there.)
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131
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132 - using one of the legacy chromosomes that doesn't include detritus
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133
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134 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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135
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136 -->
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137 <when value="preset">
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138 <param name="preset_karyotype" type="select" label="Choose your Circos karyotype" help="In parentheses are the naming conventions for chromosomes used in each karyotype file. These are required for some plot parameters (e.g. filtering chromosomes or specifying rules). The karyotype will also be output along with your plot, for your review.">
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139 <option value="karyotype.arabidopsis.tair10.txt">Arabidopsis tair10 (chr1,chr2,..)</option>
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140 <option value="karyotype.chimp.pt4.txt">Chimp pt4 (pt1,pt2a,pt2b,..)</option>
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141 <option value="karyotype.drosophila.dm6.hires.txt">Drosophila dm6 (M,X,Y,2L,2R,..)</option>
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142 <option value="karyotype.drosophila.hires.dm3.txt">Drosophila dm3 (dmX,dm2l,dm2r,..)</option>
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143 <option value="karyotype.human.hg38.txt" selected="True">Human hg38 (hs1,hs2,..,hsX,hsY)</option>
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144 <option value="karyotype.human.hg19.txt">Human hg19 (hs1,hs2,..,hsX,hsY)</option>
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145 <option value="karyotype.human.hg18.txt">Human hg18 (hs1,hs2,..,hsX,hsY)</option>
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146 <option value="karyotype.human.hg17.txt">Human hg17 (hs1,hs2,..,hsX,hsY)</option>
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147 <option value="karyotype.human.hg16.txt">Human hg16 (hs1,hs2,..,hsX,hsY)</option>
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148 <option value="karyotype.mouse.mm10.txt">Mouse mm10 (mm1,mm2,..)</option>
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149 <option value="karyotype.mouse.mm9.txt">Mouse mm9 (mm1,mm2,..)</option>
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150 <option value="karyotype.oryzasativa.txt">Oryzasativa (os1,os2,..)</option>
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151 <option value="karyotype.rat.rn4.txt">Rat rn4 (rn1,rn2,..)</option>
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152 <option value="karyotype.sorghum.txt">Sorghum (sb1,sb2,..)</option>
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153 <option value="karyotype.yeast.txt">Yeast (chrI, chrII,..)</option>
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154 <option value="karyotype.zeamays.txt">Zeamays (zm1,zm2,..)</option>
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155 </param>
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156 </when>
2
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157 <when value="cached">
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158 <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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159 <options from_data_table="__dbkeys__"/>
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160 </param>
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161 </when>
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162 <when value="history">
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163 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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164 </when>
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165 <when value="karyotype">
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166 <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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167 </when>
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168 <when value="lengths">
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169 <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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170 </when>
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171 </conditional>
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172 </section>
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173
6
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174 <section name="ideogram" title="Ideogram">
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175 <param name="limit_chromosomes" type="text" optional="true" label="Limit/Filter and Order Chromosomes" help="For example: 'hs1;hs2;hs3' or 'chr1:1-1000;chr2:3000-9000' to plot only a subset of regions. The chromosome names must match those in your karyotype file. They will be displayed in this order as well, you will need to specify all chromosomes that you wish to plot. The numerical positions are in terms of chromosome units (whatever this is set to)">
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176 <sanitizer>
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177 <valid initial="string.letters,string.digits">
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178 <add value=","/>
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179 <add value="_"/>
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180 <add value="."/>
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181 <add value=":"/>
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182 <add value=";"/>
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183 <add value="-"/>
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184 </valid>
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185 </sanitizer>
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186 </param>
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187 <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">
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188 <sanitizer>
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189 <valid initial="string.letters,string.digits">
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190 <add value=","/>
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191 <add value="_"/>
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192 <add value="."/>
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193 <add value=":"/>
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194 <add value=";"/>
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195 <add value="-"/>
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196 </valid>
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197 </sanitizer>
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198 </param>
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199
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200 <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">
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201 <option value="bases">Bases</option>
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202 <option value="kb">Kilobases</option>
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203 <option value="mb" selected="true">Megabases</option>
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204 <option value="gb">Gigabases</option>
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205 </param>
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206
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207 <param name="spacing" value="0.5" type="float" min="0" label="Spacing Between Ideograms (in chromosome units)"/>
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208 <repeat name="pairwise_spacing" title="Spacing between specific ideograms">
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209 <param name="chr1" type="text" label="Chromosome" help="as written in your karyotype file">
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210 <sanitizer>
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211 <valid initial="string.letters,string.digits">
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212 <add value="_"/>
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213 <add value="."/>
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214 <add value="-"/>
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215 </valid>
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216 </sanitizer>
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217 </param>
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218
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219 <param name="chr2" type="text" label="Chromosome" help="as written in your karyotype file">
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220 <sanitizer>
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221 <valid initial="string.letters,string.digits">
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222 <add value="_"/>
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223 <add value="."/>
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224 <add value="-"/>
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225 </valid>
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226 </sanitizer>
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227 </param>
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228
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229 <param name="spacing" type="float" min="0" label="Spacing between these two ideograms (in chromosome units)" value="1" />
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230 </repeat>
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231
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232 <param name="radius" type="float" value="0.90" label="Radius" min="0"/>
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233 <param name="thickness" type="float" value="30" label="Thickness" min="0"/>
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234 <param name="angle_offset" type="integer" min="-180" max="180" value="-90" label="Angle Offset" help="Rotate the plot such that the first ideogram is at the top center of the page."/>
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235 <param name="angle_orientation" type="select" label="Angle orientation" help="Chromosomes are plotted clockwise around the chromosome" >
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236 <option value="clockwise">Clockwise</option>
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237 <option value="counterclockwise">Counterclockwise</option>
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238 </param>
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239
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240 <section name="ideogram_labels" title="Labels">
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241 <param name="show_label" type="boolean" truevalue="yes" falsevalue="no" label="Show Label" checked="true"/>
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242 <param type="float" value="0.075" label="Radius" name="radius_offset"/>
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243 <param type="integer" value="24" label="Label Font Size" name="size"/>
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244 <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no" checked="true"
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245 help="When set to yes/true, labels will be perpendicular to the tangent of the circle at the location of the label. Otherwise, they will be parallel with the tangent of the circle"/>
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246 </section>
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247
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248 <section name="bands" title="Cytogenic Bands">
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249 <param name="show_bands" type="boolean" truevalue="yes" falsevalue="no" label="Show Cytogenic Bands?" checked="true" help="Cytogenic bands can be defined inside the karyotype file"/>
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250 <!-- Removed these based on reviewer feedback and that they are
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251 not heavily used. Re-enable upon user-request, perhaps
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252 with a more well defined use case rather than a
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253 speculative one.
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254 <param name="bands" type="data" format="tabular" optional="true" label="Cytogenetic Bands" 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'"/>
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255 <param name="convert_bands" type="boolean" truevalue="yes" falsevalue="no" label="Convert bands from BED format to circos karyotype band format" checked="true"
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256 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."/>
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257 -->
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258 <param name="fill_bands" type="boolean" truevalue="yes" falsevalue="no" label="Fill Bands" checked="true"/>
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259 <param name="band_transparency" type="integer" label="Band Transparency" value="3" min="0" max="5" help="0 is solid, 1 is the least transparent, and 5 is the most transparent"/>
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260
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261 <param type="integer" value="0" label="Band Stroke Thickness" name="band_stroke_thickness"/>
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262 <expand macro="circos_color" label="Band Stroke Color" name="band_stroke_color" value="#000000"/>
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263 </section>
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264 </section>
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265
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266 <section name="plot_options" title="General">
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267 <conditional name="background">
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268 <param name="background_select" type="select" label="Plot Background">
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269 <option value="transparent">Transparent</option>
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270 <option value="color" selected="true">Solid Color</option>
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271 </param>
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272 <when value="transparent" />
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273 <when value="color">
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274 <expand macro="circos_color" label="Background Color" name="background_color" value="#ffffff"/>
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275 </when>
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276 </conditional>
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277 <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"/>
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278 <param name="colour_profile" type="select" label="Load additional colour profiles" optional="true" help="Only useful in a tiny subset of situations">
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279 <option value="cg">Complete Genomics</option>
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280 </param>
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281 </section>
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282
2
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283 <section name="sec_tdd" title="2D Data Tracks">
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284 <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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285 <!-- Positioning -->
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286 <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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287 <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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288 <expand macro="zdepth"/>
2
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289
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290
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291 <conditional name="plot_format">
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292 <param name="plot_format_select" type="select" label="Plot Type">
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293 <option value="histogram" selected="True">Histogram</option>
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294 <option value="histogram-stacked">Stacked Histogram</option>
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295 <option value="heatmap">Heatmap</option>
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296 <option value="highlight">Highlight</option>
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297 <option value="line">Line</option>
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298 <option value="scatter">Scatter</option>
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299 <option value="tile">Tiles</option>
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300 <option value="text">Text Labels</option>
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301 <option value="connector">Connectors</option>
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302 </param>
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303 <when value="histogram">
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304 <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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305 <section name="format_specific" title="Plot Format Specific Options">
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306 <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#ffdcfc"/>
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307 <expand macro="stroke_opts"/>
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308
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309 <param name="fill_under" type="boolean" label="Fill underneath the histogram" truevalue="yes" falsevalue="no" checked="true" />
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310 <param name="extend_bins" type="boolean" label="Join non-abutting Bins" truevalue="yes" falsevalue="no"
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311 help="Join histogram bins that do not touch (abut)" />
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312 </section>
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313 </when>
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314 <when value="histogram-stacked">
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315 <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"/>
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316 <section name="format_specific" title="Plot Format Specific Options">
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317 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
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318 <expand macro="stroke_opts"/>
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319
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320 <param name="fill_under" type="boolean" label="Fill underneath the histogram" truevalue="yes" falsevalue="no" checked="true" />
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321 <param name="extend_bins" type="boolean" label="Join non-abutting Bins" truevalue="yes" falsevalue="no"
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322 help="Join histogram bins that do not touch (abut)" />
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323
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324 </section>
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325 </when>
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326 <when value="heatmap">
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327 <param name="data_source" type="data" format="tabular,interval" label="Heatmap Data Source" help="Columns must be (chrom, start, end, value)"/>
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328 <section name="format_specific" title="Plot Format Specific Options">
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329 <conditional name="color_scale">
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330 <param name="color_scale_select" type="select" label="Color Scale">
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331 <option value="basic" selected="True">Basic</option>
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332 <option value="advanced">Advanced</option>
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333 </param>
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334 <when value="basic">
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335 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
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336 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
337 <when value="advanced">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
338 <param name="fill_color" type="text" label="Advanced color entry" help="E.g. blues-5-seq-rev,reds-5-seq">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
339 <sanitizer>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
340 <valid initial="string.letters,string.digits">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
341 <add value="," />
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
342 <add value="-" />
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
343 </valid>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
344 </sanitizer>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
345 </param>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
346 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
347 </conditional>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
348 <expand macro="stroke_opts"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
349
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
350 <param name="color_mapping" type="select" label="Color Mapping">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
351 <option value="0" selected="True">divided uniformly</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
352 <option value="1">division at min/max boundary 1/2 size of others</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
353 <option value="2">divided uniformly, 0,n reserved for [,min] and [max,]</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
354 </param>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
355
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
356 <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
357 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
358 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
359 </when>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
360 <when value="highlight">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
361 <param name="data_source" type="data" format="tabular,interval" label="Highlight Data Source" help="Columns must be (chrom, start, end)"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
362 <section name="format_specific" title="Plot Format Specific Options">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
363 <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#000000"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
364 <expand macro="stroke_opts"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
365 </section>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
366 </when>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
367 <when value="line">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
368 <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
369 <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
370 <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
371 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
372 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
373 <when value="scatter">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
374 <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
375 <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
376 <!-- 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
377 <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
378 <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
379 <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
380 <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
381 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
382 <param name="glyph_size" type="integer" value="8" label="Glyph Size"/>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
383 <expand macro="circos_color_alpha" name="fill_color" value="#555555" label="Fill Color" />
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
384 <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
385 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
386 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
387 <when value="tile">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
388 <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
389 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
390 <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
391 <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
392
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
393 <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
394 <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
395 <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
396 <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
397 <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
398
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
399 <conditional name="overflow">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
400 <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
401 <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
402 <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
403 <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
404 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
405 <when value="hide">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
406 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
407 <when value="grow">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
408 <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
409 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
410 <when value="collapse">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
411 <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
412 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
413 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
414 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
415 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
416 <when value="text">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
417 <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
418
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
419 <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
420 <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
421 <conditional name="link">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
422 <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
423 <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
424 <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
425 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
426 <when value="yes">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
427 <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
428 <expand macro="circos_color" name="link_color" label="Link Color" value="#ff0000"/>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
429 <param name="link_dims" type="text" value="1p,2p,3p,2p,1p" label="Link dimensions" help="From the manual: &quot;Each link line has five dimensions: outer padding, outer line length (drawn at new position), connecting line length (connects old to new position), inner line length (drawn at old position) and inner padding. If snuggling is not used, then distinction between line lengths is not made&quot;.">
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
430 <sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
431 <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
432 <add value="p"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
433 <add value=","/>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
434 <add value="."/>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
435 </valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
436 </sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
437 </param>
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 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
440 <when value="no">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
441 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
442 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
443 <conditional name="snuggle">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
444 <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">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
445 <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
446 <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
447 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
448 <when value="yes">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
449 <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"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
450 <param name="snuggle_sampling" type="integer" value="2" min="1" label="Snuggle Sampling" help="Sample possible positions every N pixels"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
451 <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
parents:
diff changeset
452 <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"
iuc
parents:
diff changeset
453 <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)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
454 <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)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
455 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
456 <when value="no">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
457 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
458 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
459
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
460 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
461 </when>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
462 <when value="connector">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
463 <param name="data_source" type="data" format="interval" label="Connector Data Source" help="Columns must be (chrom, pos1, pos2). Connectors are articulated line segments that relate two positions on an ideogram between two radial positions."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
464 <section name="format_specific" title="Plot Format Specific Options">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
465 <expand macro="stroke_opts"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
466 <param name="connector_dims" type="text" value="0,0.3,0.4,0.3,0" label="Connector dimensions" help="From the manual: &quot;Each link line has five dimensions: outer padding, outer line length (drawn at new position), connecting line length (connects old to new position), inner line length (drawn at old position) and inner padding. If snuggling is not used, then distinction between line lengths is not made&quot;.">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
467 <sanitizer>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
468 <valid initial="string.digits">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
469 <add value=","/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
470 <add value="."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
471 </valid>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
472 </sanitizer>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
473 </param>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
474 </section>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
475 </when>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
476 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
477 <param name="orientation" type="boolean" label="Orient Inwards" truevalue="in" falsevalue="out"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
478 help="When yes, the plot will face inwards; i.e. lowest values will be plotted to the outside"/>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
479 <expand macro="minsize" />
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
480 <expand macro="minmax" />
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 <expand macro="rules" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
483 <expand macro="axes" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
484 <expand macro="backgrounds" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
485 </repeat>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
486 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
487 <section name="sec_links" title="Link Tracks">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
488 <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.">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
489 <!-- Positioning -->
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
490 <param name="radius" type="float" value="0.8" min="0" max="1" label="Inside Radius"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
491 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)" />
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
492 <expand macro="zdepth"/>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
493 <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" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
494 <conditional name="linktype">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
495 <param name="ribbon" type="select" label="Link Type" help="">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
496 <option value="no">basic</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
497 <option value="yes" selected="true">ribbon</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
498 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
499 <when value="yes">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
500 <param name="twist" type="select" label="Twist Ribbon" help="Fine grained control for display behaviour of ribbons">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
501 <option value="" selected="true">auto</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
502 <option value="twist=yes">always (twist)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
503 <option value="flat=yes">never (flat)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
504 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
505 <param name="pattern" type="select" label="Ribbon background pattern">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
506 <option value="solid" selected="true">Solid</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
507 <option value="hline">Horizontal Lines</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
508 <option value="hline-sparse">Horizontal Lines (sparse)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
509 <option value="vline">Vertical Lines</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
510 <option value="vline-sparse">Vertical Lines (sparse)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
511 <option value="checker">Checker</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
512 <option value="checker-sparse">Checker (sparse)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
513 <option value="dot">Dots</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
514 <option value="dot-sparse">Dots (sparse)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
515 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
516 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
517 <when value="no"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
518 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
519 <expand macro="circos_color_alpha" name="color" value="#000000" label="Link Color"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
520 <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
521 <param name="bezier_radius" type="float" value="0.1" min="0" max="1" label="Bezier Radius"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
522 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"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
523
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
524 <section name="advanced" title="Advanced Settings">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
525 <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"
iuc
parents:
diff changeset
526 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"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
527 <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
528 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)"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
529 <conditional name="perturbation">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
530 <param name="perturb" type="select" label="Perturb links?"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
531 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
532 <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
533 <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
534 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
535 <when value="yes">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
536 <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
537 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
538 <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
539 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
540 <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
541 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
542 <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
543 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
544 <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
545 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
546 <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
547 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
548 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
549 <when value="no"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
550 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
551 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
552 <expand macro="linkrules"/>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
553 <expand macro="minsize" />
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
554 </repeat>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
555 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
556
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
557 <section name="scaling" title="Scaling">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
558 <repeat name="zooms" title="Zoomed Region" help="From the documentation: &quot;Local adjustment of scale is for cases when you want to zoom parts of your data domain without cropping. If you think of the ideogram as a rubber band, applying a local scale adjustment is analogous to locally stretching or compressing the rubber band. The effect is that you still see the entire rubber band, but the length scale across it is variable.&quot;">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
559 <param name="chr" type="text" label="Chromosome" help="as written in your karyotype file" />
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
560
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
561 <param name="start" type="float" label="Start" value="1" help="in chromosome units" />
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
562 <param name="end" type="float" label="End" value="5" help="in chromosome units" />
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
563 <param name="scale" type="float" min="0" label="Scale" value="5" />
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
564 </repeat>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
565 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
566
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
567 <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
568 <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
569 <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
570 <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
571
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
572 <repeat name="tick_group" title="Tick Group">
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
573 <param name="spacing" type="float" min="0" label="Tick Spacing" value="1" help="in chromosome units" />
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
574 <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
575 <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
576 <conditional name="ticks">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
577 <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
578 <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
579 <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
580 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
581 <when value="yes">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
582 <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
583 <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
584 <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
585 <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
586 <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
587 <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
588 <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
589 <sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
590 <valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
591 <add value="%" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
592 </valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
593 </sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
594 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
595 <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
596 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
597 <when value="no">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
598 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
599 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
600 </repeat>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
601
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
602 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
603
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
604 <section name="limits" title="Limits">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
605 <param name="max_ticks" type="integer" min="200" value="5000" label="Maximum number of ticks to draw" help="These are advanced options, if you increase these due to a plotting failure it may result in a significantly longer plotting time. Beware!"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
606 <param name="max_ideograms" type="integer" min="200" value="200" label="Maximum number of ideograms to draw"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
607 <param name="max_links" type="integer" min="200" value="25000" label="Maximum number of links to draw"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
608 <param name="max_points_per_track" type="integer" min="200" value="25000" label="Maximum number of points per track"/>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
609 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
610
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
611 <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
612 <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
613 <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
614 <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
615 </section>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
616 </inputs>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
617 <outputs>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
618 <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
619 <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
620 </data>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
621 <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
622 <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
623 </data>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
624 <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
625 <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
626 </data>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
627 <data name="karyotype_txt" format="tabular" from_work_dir="circos/conf/karyotype.txt" label="Circos Karyotype">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
628 <filter>reference_genome['ref']['ref_source'] != 'karyotype' and reference_genome['ref']['ref_source'] != 'preset' </filter>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
629 </data>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
630 </outputs>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
631 <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
632 <help><![CDATA[
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
633 Circos
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
634 ======
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
635
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
636 .. class:: infomark
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
637
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
638 Made a nice plot? Share it with us in the `training materials <https://github.com/galaxyproject/training-material/issues/1867>`__, we're looking for more cool plots with scientifically relevant stories to share with the students who want to learn how to use Circos.
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
639
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
640 Have a feature request? `Share it with us! <https://github.com/galaxyproject/training-material/issues/1867>`__
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
641
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
642 .. class:: warningmark
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
643
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
644 No data or plot crashes? Check that your chromosome naming scheme matches between your Karyotype file and your datasets.
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 4
diff changeset
645
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
646 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"
iuc
parents:
diff changeset
647
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
648 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"
iuc
parents:
diff changeset
649
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
650 .. 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"
iuc
parents:
diff changeset
651 :alt: several example circos plots
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
652
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
653 For more information see the Circos documentation_.
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
654
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
655 .. _documentation: http://circos.ca/documentation/
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
656
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
657
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
658 ]]></help>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
659 <expand macro="citations" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents:
diff changeset
660 </tool>