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1 <tool id="oncocircos" name="Oncocircos" version="0.69">
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2
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3 <description>
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4 creates a genome-centric visualization of SNV and CNV Data
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5 </description>
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6
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7 <requirements>
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8 <requirement type="package" version="0.69">circos_perl_environment</requirement>
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9 <requirement type="package" version="0.69">circos</requirement>
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10 </requirements>
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11
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12
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13 <command error_checking="aggressive">
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14
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15 mkdir data;
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16 mkdir circos;
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17 mkdir circos/data;
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18 mkdir circos/etc;
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19
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2
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20 touch data/cnv.large.scale.txt;
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21 cat $sig_regions >> data/cnv.large.scale.txt;
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22 touch data/genes_to_label.txt;
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23 #if $advancedOptions.gene_label_input_type.gene_label_input_type_selector.value == "other":
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24 echo $advancedOptions.gene_label_input_type.gene > data/genes_to_label.txt;
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25 #else:
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26 cat $advancedOptions.gene_label_input_type.gene_file > data/genes_to_label.txt;
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27 #end if
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28
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29 touch data/genes_to_hide.txt;
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30 #if $advancedOptions.gene_mask_input_type.gene_mask_input_type_selector.value == "other":
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31 echo $advancedOptions.gene_mask_input_type.gene > data/genes_to_hide.txt;
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32 #else:
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33 cat $advancedOptions.gene_mask_input_type.gene_file > data/genes_to_hide.txt;
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34 #end if
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35
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0
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36 cp $__tool_directory__/etc/* circos/etc/;
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37
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38 mkdir etc;
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39
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40 ln -s $input_maf data/snv.txt;
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41 ln -s $input_seg data/cnv.txt;
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2
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42 ln -s $biomart data/biomart.txt;
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43 cat $__tool_directory__/parse.conf
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44
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45 #if $advancedOptions.filter_snvs != 1:
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46 | sed 's/^SNV_FILTER$/sv = yes/g'
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47 | sed 's/^SNV_FILTER_NUM$/sv_num = $advancedOptions.filter_snvs/g'
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48 #else:
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2
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49 | sed 's/^SNV_FILTER$/sv = yes/g'
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50 | sed 's/^SNV_FILTER_NUM$/sv_num = $advancedOptions.filter_snvs/g'
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0
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51 #end if
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2
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52
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0
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53 #if $advancedOptions.chromosome != "":
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54 | sed 's/^CHR$/chr = $advancedOptions.chromosome/g'
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55 #else:
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56 | sed 's/^CHR$//g'
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57 #end if
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2
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58
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0
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59
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2
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60 | sed "s#^ROOT#root = \$(pwd)#g"
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0
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61 | sed 's#^CIRCOS#circos = circos/data#g'
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62
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63 > ./etc/parse.conf;
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64
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65 perl $__tool_directory__/bin/parse --conf ./etc/parse.conf | perl $__tool_directory__/bin/make.circos.data --conf ./etc/parse.conf;
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66
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67 circos --conf ./circos/etc/circos.conf;
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68
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69 cp circos.png $png;
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70 cp circos.svg $svg;
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71 cp ./etc/parse.conf $tmp;
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72
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73 </command>
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74
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75 <inputs>
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76 <param type="data" format="maf" name="input_maf" label="Cohort Wide MAF File"/>
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77 <param type="data" format="segs" name="input_seg" label="Cohort Wide SEGS File"/>
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2
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78 <param type="data" format="" name="biomart" label="Biomart File listing all genes (format: ENSG, chrom, start, end, Symbol"/>
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79 <param type="data" format="bed" name="sig_regions" label="Regions of recurrent copy number gain/loss in bed format. 4th column must indicate the event type (e.g gain, hetd)" optional="true"/>
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0
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80 <section name="advancedOptions">
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81 <param type="integer" name="filter_snvs"
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82 min="1" value="1" max="100"
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83 label="Filter genes with a cohort wide snv tally below this value"/>
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84 <param type="text" name="chromosome" value=""
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2
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85 label="Restrict plot to the following chromosome"/>
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86 <conditional name="gene_label_input_type">
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87 <param name="gene_label_input_type_selector" type="select" label="How will you supply genes of interest to label in the plot?">
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88 <option value="file" selected="True">Gene File</option>
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89 <option value="other">Other</option>
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90 </param>
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91 <when value="file">
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92 <param name="gene_file" type="data" format="txt" label="Gene File" help="list of genes separated by newlines" />
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93 </when>
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94 <when value="other">
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95 <param name="gene" type="text" value="TP53" label="Gene" help="type the single gene" />
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96 </when>
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97 </conditional>
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98 <conditional name="gene_mask_input_type">
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99 <param name="gene_mask_input_type_selector" type="select" label="How will you supply blacklist genes to hide from plot?">
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100 <option value="file" selected="True">Gene Blacklist File</option>
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101 <option value="other">Other</option>
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102 </param>
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103 <when value="file">
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104 <param name="gene_file" type="data" format="txt" label="Gene File" help="list of genes separated by newlines" />
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105 </when>
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106 <when value="other">
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107 <param name="gene" type="text" value="TP53" label="Gene" help="type the single gene" />
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108 </when>
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109 </conditional>
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0
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110 </section>
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111 </inputs>
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112 <outputs>
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113 <data format="png" name="png" />
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114 <data format="svg" name="svg" />
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115 <data format="txt" name="tmp" />
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116 </outputs>
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2
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117 <citations>
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118 <citation type="bibtex">
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119 @article {Albuquerque089631,
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120 author = {Albuquerque, Marco A and Grande, Bruno M and Ritch, Elie and Jessa, Selin and Krzywinski, Martin I and Grewal, Jasleen and Shah, Sohrab and Boutros, Paul and Morin, Ryan},
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121 title = {Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy},
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122 year = {2016},
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123 doi = {10.1101/089631},
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124 publisher = {Cold Spring Harbor Labs Journals},
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125 URL = {http://biorxiv.org/content/early/2016/11/26/089631},
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126 eprint = {http://biorxiv.org/content/early/2016/11/26/089631.full.pdf},
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127 journal = {bioRxiv}
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128 }
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129
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130 </citation>
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131 <citation type="bibtex">
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132 @misc{
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133 goecks2010galaxy,
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134 title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
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135 author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and others},
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136 journal={Genome Biol},
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137 volume={11},
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138 number={8},
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139 pages={R86},
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140 year={2010}
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141 }
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142 </citation>
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143 <citation type="bibtex">
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144
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145 @ARTICLE{Krzywinski2009-hn,
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146 title = "Circos: an information aesthetic for comparative genomics",
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147 author = "Krzywinski, Martin and Schein, Jacqueline and Birol, Inan\c{c}
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148 and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and
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149 Jones, Steven J and Marra, Marco A",
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150 affiliation = "Canada's Michael Smith Genome Sciences Center, Vancouver,
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151 British Columbia V5Z 4S6, Canada. martink@bcgsc.ca",
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152 abstract = "We created a visualization tool called Circos to facilitate
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153 the identification and analysis of similarities and
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154 differences arising from comparisons of genomes. Our tool is
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155 effective in displaying variation in genome structure and,
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156 generally, any other kind of positional relationships between
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157 genomic intervals. Such data are routinely produced by
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158 sequence alignments, hybridization arrays, genome mapping, and
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159 genotyping studies. Circos uses a circular ideogram layout to
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160 facilitate the display of relationships between pairs of
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161 positions by the use of ribbons, which encode the position,
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162 size, and orientation of related genomic elements. Circos is
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163 capable of displaying data as scatter, line, and histogram
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164 plots, heat maps, tiles, connectors, and text. Bitmap or
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165 vector images can be created from GFF-style data inputs and
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166 hierarchical configuration files, which can be easily
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167 generated by automated tools, making Circos suitable for rapid
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168 deployment in data analysis and reporting pipelines.",
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169 journal = "Genome Res.",
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170 volume = 19,
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171 number = 9,
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172 pages = "1639--1645",
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173 month = sep,
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174 year = 2009,
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175 language = "en"
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176 }
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177
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178
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179 </citation>
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180 </citations>
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181 </tool>
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