Mercurial > repos > jjohnson > arriba_download_reference

annotate macros.xml @ 0:7345cb1bb772 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
author jjohnson
date Fri, 11 Feb 2022 19:09:19 +0000
parents
children 55ca46d68a57
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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>
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2 <token name="@TOOL_VERSION@">2.2.1</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">
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52 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
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53 <help>By default the transcript isoform with the highest coverage is drawn.
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54 Alternatively, the transcript isoform that is provided in the columns
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55 transcript_id1 and transcript_id2 in the given fusions file can be drawn.
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56 Selecting the isoform with the highest coverage usually produces nicer plots,
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57 in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint.
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58 However, the isoform with the highest coverage may not be the one that is involved in the fusion.
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59 Often, genomic rearrangements lead to non-canonical isoforms being transcribed.
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60 For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2,
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61 which reflect the actual isoforms involved in a fusion.
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62 \ As a third option, the transcripts that are annotated as canonical can be drawn.
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63 Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.
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64 </help>
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65 <option value="coverage">coverage</option>
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66 <option value="provided">provided</option>
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67 <option value="canonical">canonical</option>
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68 </param>
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69 <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection">
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70 <help>The fusion of interest is drawn as a solid line in the circos plot.
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71 To give an impression of the overall degree of rearrangement,
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72 all other fusions are drawn as semi-transparent lines in the background.
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73 This option determines which other fusions should be included in the circos plot.
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74 Values specify the minimum confidence a fusion must have to be included.
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75 It usually makes no sense to include low-confidence fusions in circos plots,
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76 because they are abundant and unreliable, and would clutter up the circos plot.
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77 Default: medium
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78 </help>
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79 <option value="none">none - only the fusion of interest is drawn</option>
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80 <option value="low">low</option>
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81 <option value="medium">medium</option>
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82 <option value="high">high</option>
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83 </param>
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84 <param argument="--showIntergenicVicinity" type="integer" value="" min="0" optional="true" label="Intergenic Vicinity">
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85 <help>This option only applies to intergenic breakpoints.
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86 If it is set to a value greater than 0, then the script draws the genes
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87 which are no more than the given distance away from an intergenic breakpoint.
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88 Note that this option is incompatible with squishIntrons.
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89 Default: 0
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90 </help>
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91 </param>
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92 <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
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93 <help>Exons usually make up only a small fraction of a gene.
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94 They may be hard to see in the plot. i
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95 Since introns are in most situations of no interest in the context of gene fusions,
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96 this switch can be used to shrink the size of introns to a fixed, negligible size.
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97 It makes sense to disable this feature, if breakpoints in introns are of importance.
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98 Default: TRUE
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99 </help>
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100 <option value="TRUE">True</option>
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101 <option value="FALSE">False</option>
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102 </param>
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103
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104 <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
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105 <help>Occasionally, domains are annotated redundantly.
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106 For example, tyrosine kinase domains are frequently annotated as
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107 Protein tyrosine kinase and Protein kinase domain.
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108 In order to simplify the visualization, such domains can be merged into one,
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109 given that they overlap by the given fraction.
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110 The description of the larger domain is used.
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111 Default: 0.9
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112 </help>
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113 </param>
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114 <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels">
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115 <help>By default the number of an exon is printed inside each exon,
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116 which is taken from the attribute exon_number of the GTF annotation.
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117 When a gene has many exons, the boxes may be too narrow to contain the labels,
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118 resulting in unreadable exon labels. In these situations, i
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119 it may be better to turn off exon labels.
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120 Default: TRUE
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121 </help>
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122 <option value="TRUE">True</option>
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123 <option value="FALSE">False</option>
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124 </param>
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125 <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect">
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126 <help>Whether light and shadow should be rendered to give objects a 3D effect.
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127 Default: TRUE
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128 </help>
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129 <option value="TRUE">True</option>
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130 <option value="FALSE">False</option>
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131 </param>
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132 <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors">
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133 <help>By default, the script colorizes domains according to the colors
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134 specified in the file given in --annotation.
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135 This way, coloring of domains is consistent across all proteins.
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136 But since there are more distinct domains than colors,
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137 this can lead to different domains having the same color.
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138 If this option is set to TRUE, the colors are recomputed for each fusion separately.
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139 This ensures that the colors have the maximum distance for each individual fusion,
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140 but they are no longer consistent across different fusions.
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141 Default: FALSE
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142 </help>
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143 <option value="TRUE">True</option>
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144 <option value="FALSE">False</option>
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145 </param>
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146 <param argument="--color1" type="color" value="" optional="true" label="Color of the 5' end of the fusion."/>
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147 <param argument="--color2" type="color" value="" optional="true" label="Color of the 3' end of the fusion."/>
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148 <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"
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149 help="Default: 11.692"/>
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150 <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
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151 help="Default: 8.267"/>
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152 <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
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153 help="Default: 1.0"/>
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154 </section>
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155 </xml>
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156 <token name="@DRAW_FUSIONS@">
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157 draw_fusions.R
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158 --fusions='$fusions'
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159 --alignments='Aligned.sortedByCoord.out.bam'
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160 --annotation='$genome.annotation'
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161 --output=fusions.pdf
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162 #if $visualization.cytobands
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163 --cytobands='$visualization.cytobands'
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164 #end if
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165 #if $protein_domains
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166 --proteinDomains='$protein_domains'
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167 #end if
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168 ## Visualization Options
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169 #if $visualization.options.transcriptSelection
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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170 --transcriptSelection=$visualization.options.transcriptSelection
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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171 #end if
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jjohnson
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172 #if $visualization.options.minConfidenceForCircosPlot
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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173 --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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174 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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175 #if $visualization.options.showIntergenicVicinity
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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176 --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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177 #end if
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178 #if $visualization.options.squishIntrons
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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179 --squishIntrons=$visualization.options.squishIntrons
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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180 #end if
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181 #if $visualization.options.mergeDomainsOverlappingBy
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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182 --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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183 #end if
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184 #if $visualization.options.printExonLabels
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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185 --printExonLabels=$visualization.options.printExonLabels
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186 #end if
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187 #if $visualization.options.render3dEffect
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188 --render3dEffect=$visualization.options.render3dEffect
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189 #end if
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190 #if $visualization.options.optimizeDomainColors
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191 --optimizeDomainColors=$visualization.options.optimizeDomainColors
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192 #end if
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193 #if $visualization.options.color1
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194 --color1=$visualization.options.color1
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195 #end if
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196 #if $visualization.options.color2
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197 --color2=$visualization.options.color2
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198 #end if
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199 #if $visualization.options.pdfWidth
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200 --pdfWidth=$visualization.options.pdfWidth
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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201 #end if
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202 #if $visualization.options.pdfHeight
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203 --pdfHeight=$visualization.options.pdfHeight
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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204 #end if
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205 #if $visualization.options.fontSize
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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206 --fontSize=$visualization.options.fontSize
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207 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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208 </token>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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209 </macros>