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comparison macros.xml @ 0:2d4e3aff9dc7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
author iuc
date Wed, 27 Jul 2022 11:25:43 +0000
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children cf18a5993aa2
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-1:000000000000 0:2d4e3aff9dc7
1 <macros>
2 <token name="@TOOL_VERSION@">2.3.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
7 <yield/>
8 </requirements>
9 </xml>
10 <xml name="citations">
11 <citations>
12 <citation type="doi">10.1101/gr.257246.119</citation>
13 <yield />
14 </citations>
15 </xml>
16 <xml name="version_command">
17 <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
18 </xml>
19 <xml name="genome_source" token_assembly_optional="false" >
20 <conditional name="genome">
21 <param name="genome_source" type="select" label="Genome assembly fasta (that was used for STAR alignment)">
22 <option value="history">From your history</option>
23 <option value="cached">Use built-in Genome reference</option>
24 </param>
25 <when value="history">
26 <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/>
27 </when>
28 <when value="cached">
29 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
30 <options from_data_table="all_fasta">
31 <validator type="no_options" message="No reference genomes are available" />
32 </options>
33 </param>
34 </when>
35 </conditional>
36 </xml>
37 <xml name="gtf_source" token_assembly_optional="false" >
38 <conditional name="genome_gtf">
39 <param name="gtf_source" type="select" label="Genome GTF annotation source">
40 <option value="history">From your history</option>
41 <!-- <option value="cached">Use built-in Gtf annotation</option> -->
42 </param>
43 <when value="history">
44 <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/>
45 </when>
46 </conditional>
47 </xml>
48
49 <token name="@GENOME_SOURCE@"><![CDATA[
50 #if str($genome.genome_source) == "history"
51 #if $genome.assembly
52 #set $genome_assembly = 'genome.fa'
53 ln -sf '$genome.assembly' $genome_assembly &&
54 #end if
55 #elif str($genome.genome_source) == "cached"
56 #set $genome_assembly = $genome.ref_file.fields.fasta
57 #end if
58 ]]></token>
59 <token name="@GTF_SOURCE@"><![CDATA[
60 #if str($genome_gtf.gtf_source) == "history"
61 #if $genome_gtf.annotation.is_of_type('gtf.gz')
62 #set $genome_annotation = 'genome.gtf.gz'
63 #else
64 #set $genome_annotation = 'genome.gtf'
65 #end if
66 ln -sf '$genome_gtf.annotation' $genome_annotation &&
67 #end if
68 ]]></token>
69
70 <xml name="visualization_options">
71 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
72 <section name="options" expanded="false" title="Draw Fusion Options">
73 <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>
74 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
75 <help>By default the transcript isoform with the highest coverage is drawn.
76 Alternatively, the transcript isoform that is provided in the columns
77 transcript_id1 and transcript_id2 in the given fusions file can be drawn.
78 Selecting the isoform with the highest coverage usually produces nicer plots,
79 in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint.
80 However, the isoform with the highest coverage may not be the one that is involved in the fusion.
81 Often, genomic rearrangements lead to non-canonical isoforms being transcribed.
82 For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2,
83 which reflect the actual isoforms involved in a fusion.
84 \ As a third option, the transcripts that are annotated as canonical can be drawn.
85 Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.
86 </help>
87 <option value="coverage">coverage</option>
88 <option value="provided">provided</option>
89 <option value="canonical">canonical</option>
90 </param>
91 <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection">
92 <help>The fusion of interest is drawn as a solid line in the circos plot.
93 To give an impression of the overall degree of rearrangement,
94 all other fusions are drawn as semi-transparent lines in the background.
95 This option determines which other fusions should be included in the circos plot.
96 Values specify the minimum confidence a fusion must have to be included.
97 It usually makes no sense to include low-confidence fusions in circos plots,
98 because they are abundant and unreliable, and would clutter up the circos plot.
99 Default: medium
100 </help>
101 <option value="none">none - only the fusion of interest is drawn</option>
102 <option value="low">low</option>
103 <option value="medium">medium</option>
104 <option value="high">high</option>
105 </param>
106 <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
107 <help>Exons usually make up only a small fraction of a gene.
108 They may be hard to see in the plot. i
109 Since introns are in most situations of no interest in the context of gene fusions,
110 this switch can be used to shrink the size of introns to a fixed, negligible size.
111 It makes sense to disable this feature, if breakpoints in introns are of importance.
112 Default: TRUE
113 </help>
114 <option value="TRUE">True</option>
115 <option value="FALSE">False</option>
116 </param>
117 <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity">
118 <help>This option only applies to intergenic breakpoints.
119 If it is set to a value greater than 0, then the script draws the genes
120 which are no more than the given distance away from an intergenic breakpoint.
121 The keywords closestGene and closestProteinCodingGene instruct the script
122 to dynamically determine the distance to the next (protein-coding) gene for each breakpoint.
123 Alternatively, instead of specifying a single distance
124 that is applied upstream and downstream of both breakpoints alike,
125 more fine-grained control over the region to be shown is possible by specifying four comma-separated values.
126 The first two values determine the region to the left and to the right of breakpoint 1;
127 the third and fourth values determine the region to the left and to the right of breakpoint 2.
128 Note that this option is incompatible with squishIntrons.
129 Default: 0
130 </help>
131 <option value="closestGene">closestGene</option>
132 <option value="closestProteinCodingGene">closestProteinCodingGene</option>
133 <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$</validator>
134 </param>
135 <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
136 <help>Occasionally, domains are annotated redundantly.
137 For example, tyrosine kinase domains are frequently annotated as
138 Protein tyrosine kinase and Protein kinase domain.
139 In order to simplify the visualization, such domains can be merged into one,
140 given that they overlap by the given fraction.
141 The description of the larger domain is used.
142 Default: 0.9
143 </help>
144 </param>
145 <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels">
146 <help>By default the number of an exon is printed inside each exon,
147 which is taken from the attribute exon_number of the GTF annotation.
148 When a gene has many exons, the boxes may be too narrow to contain the labels,
149 resulting in unreadable exon labels. In these situations, i
150 it may be better to turn off exon labels.
151 Default: TRUE
152 </help>
153 <option value="TRUE">True</option>
154 <option value="FALSE">False</option>
155 </param>
156 <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect">
157 <help>Whether light and shadow should be rendered to give objects a 3D effect.
158 Default: TRUE
159 </help>
160 <option value="TRUE">True</option>
161 <option value="FALSE">False</option>
162 </param>
163 <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors">
164 <help>By default, the script colorizes domains according to the colors
165 specified in the file given in --annotation.
166 This way, coloring of domains is consistent across all proteins.
167 But since there are more distinct domains than colors,
168 this can lead to different domains having the same color.
169 If this option is set to TRUE, the colors are recomputed for each fusion separately.
170 This ensures that the colors have the maximum distance for each individual fusion,
171 but they are no longer consistent across different fusions.
172 Default: FALSE
173 </help>
174 <option value="TRUE">True</option>
175 <option value="FALSE">False</option>
176 </param>
177 <param argument="--color1" type="color" value="" optional="true" label="Color of the 5' end of the fusion."/>
178 <param argument="--color2" type="color" value="" optional="true" label="Color of the 3' end of the fusion."/>
179 <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"
180 help="Default: 11.692"/>
181 <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
182 help="Default: 8.267"/>
183 <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
184 help="Default: 1.0"/>
185 <param argument="--fontFamily" type="text" value="" optional="true" label="Font to use for all labels in the plots.">
186 <help>Default: Helvetica
187 </help>
188 <option value="serif">serif</option>
189 <option value="sans">sans</option>
190 <option value="mono">mono</option>
191 <option value="AvantGarde">AvantGarde</option>
192 <option value="Bookman">Bookman</option>
193 <option value="Courier">Courier</option>
194 <option value="Helvetica">Helvetica</option>
195 <option value="Helvetica-Narrow">Helvetica-Narrow</option>
196 <option value="NewCenturySchoolbook">NewCenturySchoolbook</option>
197 <option value="Palatino">Palatino</option>
198 <option value="Times">Times</option>
199 <option value="URWGothic">URWGothic</option>
200 <option value="URWBookman">URWBookman</option>
201 <option value="NimbusMon">NimbusMon</option>
202 <option value="NimbusSan">NimbusSan</option>
203 <option value="URWHelvetica">URWHelvetica</option>
204 <option value="NimbusSanCond">NimbusSanCond</option>
205 <option value="CenturySch">CenturySch</option>
206 <option value="URWPalladio">URWPalladio</option>
207 <option value="NimbusRom">NimbusRom</option>
208 <option value="URWTimes">URWTimes</option>
209 <option value="ArialMT">ArialMT</option>
210 <option value="Japan1">Japan1</option>
211 <option value="Japan1HeiMin">Japan1HeiMin</option>
212 <option value="Japan1GothicBBB">Japan1GothicBBB</option>
213 <option value="Japan1Ryumin">Japan1Ryumin</option>
214 <option value="Korea1">Korea1</option>
215 <option value="Korea1deb">Korea1deb</option>
216 <option value="CNS1">CNS1</option>
217 <option value="GB1">GB1</option>
218 </param>
219 <param argument="--fixedScale" type="integer" value="" min="0" optional="true" label="Apply a fixed scale to all fusions">
220 <help>By default, transcripts are scaled automatically to fill the entire page.
221 This parameter enforces a fixed scale to be applied to all fusions,
222 which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable.
223 A common use case is the visualization of a gene that is found to be fused to multiple partners.
224 By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage
225 in a single plot one above the other with matching scales.
226 Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn,
227 or else dynamic scaling is applied, because display errors would occur otherwise.
228 The default value is 0, which means that no fixed scale should be used
229 and that the scale should be adapted dynamically for each fusion. Default: 0
230 </help>
231 </param>
232 <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot">
233 <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes.
234 The plots can be cropped at a fixed level by passing a non-zero value to this parameter.
235 When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level.
236 When two comma-separated values are given, the cutoffs can be specified independently for the two plots.
237 A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage)
238 and that the coverage plots of both genes should be on the same scale. This is the default behavior.
239 A value of 0,0 also indicates that no cropping should be applied,
240 but the coverage plots of the two genes have different scales:
241 each one is scaled individually to the peak coverage of the respective gene.
242 Default: 0
243 </help>
244 <validator type="regex" message="">^\d+(,\d+)?$</validator>
245 </param>
246 </section>
247 </xml>
248 <token name="@DRAW_FUSIONS@">
249 draw_fusions.R
250 --fusions='$fusions'
251 --alignments='Aligned.sortedByCoord.out.bam'
252 --annotation='$genome_gtf.annotation'
253 --output=fusions.pdf
254 #if $visualization.cytobands
255 --cytobands='$visualization.cytobands'
256 #end if
257 #if $protein_domains
258 --proteinDomains='$protein_domains'
259 #end if
260 ## Visualization Options
261 #if $visualization.options.transcriptSelection
262 --transcriptSelection=$visualization.options.transcriptSelection
263 #end if
264 #if $visualization.options.minConfidenceForCircosPlot
265 --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
266 #end if
267 #if $visualization.options.squishIntrons
268 --squishIntrons=$visualization.options.squishIntrons
269 #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity
270 --showIntergenicVicinity='$visualization.options.showIntergenicVicinity'
271 #end if
272 #end if
273 #if $visualization.options.mergeDomainsOverlappingBy
274 --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
275 #end if
276 #if $visualization.options.sampleName
277 --sampleName='$visualization.options.sampleName'
278 #end if
279 #if $visualization.options.printExonLabels
280 --printExonLabels=$visualization.options.printExonLabels
281 #end if
282 #if $visualization.options.coverageRange
283 --coverageRange='$visualization.options.coverageRange'
284 #end if
285 #if $visualization.options.render3dEffect
286 --render3dEffect=$visualization.options.render3dEffect
287 #end if
288 #if $visualization.options.optimizeDomainColors
289 --optimizeDomainColors=$visualization.options.optimizeDomainColors
290 #end if
291 #if $visualization.options.color1
292 --color1='$visualization.options.color1'
293 #end if
294 #if $visualization.options.color2
295 --color2='$visualization.options.color2'
296 #end if
297 #if str($visualization.options.pdfWidth)
298 --pdfWidth=$visualization.options.pdfWidth
299 #end if
300 #if str($visualization.options.pdfHeight)
301 --pdfHeight=$visualization.options.pdfHeight
302 #end if
303 # fontFamily
304 #if $visualization.options.fontFamily
305 --fontFamily=$visualization.options.fontFamily
306 #end if
307 #if str($visualization.options.fontSize)
308 --fontSize=$visualization.options.fontSize
309 #end if
310 </token>
311 </macros>