Mercurial > repos > jjohnson > arriba_download_reference

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
author jjohnson
date Mon, 13 Jun 2022 12:10:34 +0000
parents 7345cb1bb772
children
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7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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1 <macros>
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
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2 <token name="@TOOL_VERSION@">2.3.0</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <xml name="citations">
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11 <citations>
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12 <citation type="doi">10.1101/gr.257246.119</citation>
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13 <yield />
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14 </citations>
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15 </xml>
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16 <xml name="version_command">
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17 <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
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18 </xml>
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19 <xml name="genome_source" token_assembly_optional="false" >
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20 <conditional name="genome">
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21 <param name="genome_source" type="select" label="Arriba Genome assembly and annotation source">
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22 <option value="history">From your history</option>
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23 <option value="cached">Use built-in Arriba</option>
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24 </param>
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25 <when value="history">
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26 <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/>
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27 <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/>
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28 </when>
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29 <when value="cached">
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30 <param name="arriba_ref" type="select" label="Arriba Genome assembly and annotation">
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31 <options from_data_table="arriba_indexes">
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32 </options>
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33 </param>
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34 </when>
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35 </conditional>
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36 </xml>
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37 <token name="@GENOME_SOURCE@">
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38 #if str($genome.genome_source) == "history"
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39 #if $genome.assembly
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40 #set $genome_assembly = $genome.assembly
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41 #end if
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42 #set $genome_annotation = $genome.annotation
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43 #else
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44 #set $genome_assembly = $genome.arriba_ref.fields.fasta
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45 #set $genome_annotation = $genome.arriba_ref.fields.gtf
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46 #end if
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47 </token>
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48
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49 <xml name="visualization_options">
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50 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
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51 <section name="options" expanded="false" title="Draw Fusion Options">
1
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52 <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>
0
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53 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
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54 <help>By default the transcript isoform with the highest coverage is drawn.
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55 Alternatively, the transcript isoform that is provided in the columns
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56 transcript_id1 and transcript_id2 in the given fusions file can be drawn.
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57 Selecting the isoform with the highest coverage usually produces nicer plots,
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58 in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint.
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59 However, the isoform with the highest coverage may not be the one that is involved in the fusion.
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60 Often, genomic rearrangements lead to non-canonical isoforms being transcribed.
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61 For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2,
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62 which reflect the actual isoforms involved in a fusion.
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63 \ As a third option, the transcripts that are annotated as canonical can be drawn.
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64 Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.
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65 </help>
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66 <option value="coverage">coverage</option>
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67 <option value="provided">provided</option>
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68 <option value="canonical">canonical</option>
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69 </param>
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70 <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection">
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71 <help>The fusion of interest is drawn as a solid line in the circos plot.
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72 To give an impression of the overall degree of rearrangement,
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73 all other fusions are drawn as semi-transparent lines in the background.
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74 This option determines which other fusions should be included in the circos plot.
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75 Values specify the minimum confidence a fusion must have to be included.
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76 It usually makes no sense to include low-confidence fusions in circos plots,
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77 because they are abundant and unreliable, and would clutter up the circos plot.
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78 Default: medium
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79 </help>
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80 <option value="none">none - only the fusion of interest is drawn</option>
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81 <option value="low">low</option>
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82 <option value="medium">medium</option>
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83 <option value="high">high</option>
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84 </param>
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85 <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
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86 <help>Exons usually make up only a small fraction of a gene.
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87 They may be hard to see in the plot. i
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88 Since introns are in most situations of no interest in the context of gene fusions,
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89 this switch can be used to shrink the size of introns to a fixed, negligible size.
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90 It makes sense to disable this feature, if breakpoints in introns are of importance.
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91 Default: TRUE
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92 </help>
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93 <option value="TRUE">True</option>
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94 <option value="FALSE">False</option>
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95 </param>
1
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96 <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity">
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97 <help>This option only applies to intergenic breakpoints.
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98 If it is set to a value greater than 0, then the script draws the genes
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99 which are no more than the given distance away from an intergenic breakpoint.
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100 The keywords closestGene and closestProteinCodingGene instruct the script
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101 to dynamically determine the distance to the next (protein-coding) gene for each breakpoint.
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102 Alternatively, instead of specifying a single distance
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103 that is applied upstream and downstream of both breakpoints alike,
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104 more fine-grained control over the region to be shown is possible by specifying four comma-separated values.
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105 The first two values determine the region to the left and to the right of breakpoint 1;
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106 the third and fourth values determine the region to the left and to the right of breakpoint 2.
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107 Note that this option is incompatible with squishIntrons.
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108 Default: 0
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109 </help>
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110 <option value="closestGene">closestGene</option>
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111 <option value="closestProteinCodingGene">closestProteinCodingGene</option>
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112 <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$</validator>
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113 </param>
0
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114 <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
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115 <help>Occasionally, domains are annotated redundantly.
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116 For example, tyrosine kinase domains are frequently annotated as
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117 Protein tyrosine kinase and Protein kinase domain.
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118 In order to simplify the visualization, such domains can be merged into one,
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119 given that they overlap by the given fraction.
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120 The description of the larger domain is used.
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121 Default: 0.9
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122 </help>
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123 </param>
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124 <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels">
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125 <help>By default the number of an exon is printed inside each exon,
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126 which is taken from the attribute exon_number of the GTF annotation.
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127 When a gene has many exons, the boxes may be too narrow to contain the labels,
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128 resulting in unreadable exon labels. In these situations, i
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129 it may be better to turn off exon labels.
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130 Default: TRUE
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131 </help>
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132 <option value="TRUE">True</option>
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133 <option value="FALSE">False</option>
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134 </param>
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135 <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect">
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136 <help>Whether light and shadow should be rendered to give objects a 3D effect.
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137 Default: TRUE
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138 </help>
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139 <option value="TRUE">True</option>
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140 <option value="FALSE">False</option>
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141 </param>
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142 <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors">
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143 <help>By default, the script colorizes domains according to the colors
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144 specified in the file given in --annotation.
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145 This way, coloring of domains is consistent across all proteins.
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146 But since there are more distinct domains than colors,
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147 this can lead to different domains having the same color.
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148 If this option is set to TRUE, the colors are recomputed for each fusion separately.
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149 This ensures that the colors have the maximum distance for each individual fusion,
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150 but they are no longer consistent across different fusions.
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151 Default: FALSE
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152 </help>
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153 <option value="TRUE">True</option>
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154 <option value="FALSE">False</option>
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155 </param>
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156 <param argument="--color1" type="color" value="" optional="true" label="Color of the 5' end of the fusion."/>
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157 <param argument="--color2" type="color" value="" optional="true" label="Color of the 3' end of the fusion."/>
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158 <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"
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159 help="Default: 11.692"/>
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160 <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
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161 help="Default: 8.267"/>
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162 <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
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163 help="Default: 1.0"/>
1
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164 <param argument="--fontFamily" type="text" value="" optional="true" label="Font to use for all labels in the plots.">
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165 <help>Default: Helvetica
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166 </help>
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167 <option value="serif">serif</option>
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168 <option value="sans">sans</option>
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169 <option value="mono">mono</option>
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170 <option value="AvantGarde">AvantGarde</option>
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171 <option value="Bookman">Bookman</option>
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172 <option value="Courier">Courier</option>
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173 <option value="Helvetica">Helvetica</option>
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174 <option value="Helvetica-Narrow">Helvetica-Narrow</option>
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175 <option value="NewCenturySchoolbook">NewCenturySchoolbook</option>
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176 <option value="Palatino">Palatino</option>
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177 <option value="Times">Times</option>
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178 <option value="URWGothic">URWGothic</option>
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179 <option value="URWBookman">URWBookman</option>
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180 <option value="NimbusMon">NimbusMon</option>
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181 <option value="NimbusSan">NimbusSan</option>
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182 <option value="URWHelvetica">URWHelvetica</option>
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183 <option value="NimbusSanCond">NimbusSanCond</option>
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184 <option value="CenturySch">CenturySch</option>
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185 <option value="URWPalladio">URWPalladio</option>
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186 <option value="NimbusRom">NimbusRom</option>
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187 <option value="URWTimes">URWTimes</option>
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188 <option value="ArialMT">ArialMT</option>
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189 <option value="Japan1">Japan1</option>
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190 <option value="Japan1HeiMin">Japan1HeiMin</option>
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191 <option value="Japan1GothicBBB">Japan1GothicBBB</option>
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192 <option value="Japan1Ryumin">Japan1Ryumin</option>
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193 <option value="Korea1">Korea1</option>
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194 <option value="Korea1deb">Korea1deb</option>
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195 <option value="CNS1">CNS1</option>
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196 <option value="GB1">GB1</option>
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197 </param>
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198 <param argument="--fixedScale" type="integer" value="" min="0" optional="true" label="Apply a fixed scale to all fusions">
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199 <help>By default, transcripts are scaled automatically to fill the entire page.
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200 This parameter enforces a fixed scale to be applied to all fusions,
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201 which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable.
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202 A common use case is the visualization of a gene that is found to be fused to multiple partners.
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203 By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage
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204 in a single plot one above the other with matching scales.
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205 Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn,
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206 or else dynamic scaling is applied, because display errors would occur otherwise.
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207 The default value is 0, which means that no fixed scale should be used
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208 and that the scale should be adapted dynamically for each fusion. Default: 0
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209 </help>
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210 </param>
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211 <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot">
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212 <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes.
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213 The plots can be cropped at a fixed level by passing a non-zero value to this parameter.
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214 When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level.
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215 When two comma-separated values are given, the cutoffs can be specified independently for the two plots.
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216 A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage)
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217 and that the coverage plots of both genes should be on the same scale. This is the default behavior.
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218 A value of 0,0 also indicates that no cropping should be applied,
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219 but the coverage plots of the two genes have different scales:
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220 each one is scaled individually to the peak coverage of the respective gene.
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221 Default: 0
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222 </help>
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223 <validator type="regex" message="">^\d+(,\d+)?$</validator>
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224 </param>
0
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225 </section>
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226 </xml>
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227 <token name="@DRAW_FUSIONS@">
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228 draw_fusions.R
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229 --fusions='$fusions'
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230 --alignments='Aligned.sortedByCoord.out.bam'
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231 --annotation='$genome.annotation'
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232 --output=fusions.pdf
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233 #if $visualization.cytobands
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234 --cytobands='$visualization.cytobands'
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235 #end if
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236 #if $protein_domains
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237 --proteinDomains='$protein_domains'
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238 #end if
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239 ## Visualization Options
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240 #if $visualization.options.transcriptSelection
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241 --transcriptSelection=$visualization.options.transcriptSelection
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242 #end if
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243 #if $visualization.options.minConfidenceForCircosPlot
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244 --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
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245 #end if
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246 #if $visualization.options.squishIntrons
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247 --squishIntrons=$visualization.options.squishIntrons
1
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248 #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity
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249 --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
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250 #end if
0
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251 #end if
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252 #if $visualization.options.mergeDomainsOverlappingBy
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
253 --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
254 #end if
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
255 #if $visualization.options.sampleName
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
256 --sampleName=$visualization.options.sampleName
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
257 #end if
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
258 #if $visualization.options.printExonLabels
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
259 --printExonLabels=$visualization.options.printExonLabels
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
260 #end if
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
261 #if $visualization.options.coverageRange
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
262 --coverageRange="$visualization.options.coverageRange"
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
263 #end if
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
264 #if $visualization.options.render3dEffect
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
265 --render3dEffect=$visualization.options.render3dEffect
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
266 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
267 #if $visualization.options.optimizeDomainColors
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
268 --optimizeDomainColors=$visualization.options.optimizeDomainColors
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
269 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
270 #if $visualization.options.color1
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
271 --color1=$visualization.options.color1
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
272 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
273 #if $visualization.options.color2
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
274 --color2=$visualization.options.color2
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
275 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
276 #if $visualization.options.pdfWidth
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
277 --pdfWidth=$visualization.options.pdfWidth
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
278 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
279 #if $visualization.options.pdfHeight
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
280 --pdfHeight=$visualization.options.pdfHeight
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
281 #end if
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
282 # fontFamily
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
283 #if $visualization.options.fontFamily
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
284 --fontFamily=$visualization.options.fontFamily
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
285 #end if
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
286 #if $visualization.options.fontSize
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
287 --fontSize=$visualization.options.fontSize
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
288 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
289 </token>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
290 </macros>