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comparison macros.xml @ 1:55ca46d68a57 draft default tip

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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
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0:7345cb1bb772 1:55ca46d68a57
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.2.1</token> 2 <token name="@TOOL_VERSION@">2.3.0</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
7 <yield/> 7 <yield/>
47 </token> 47 </token>
48 48
49 <xml name="visualization_options"> 49 <xml name="visualization_options">
50 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> 50 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
51 <section name="options" expanded="false" title="Draw Fusion Options"> 51 <section name="options" expanded="false" title="Draw Fusion Options">
52 <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>
52 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection"> 53 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
53 <help>By default the transcript isoform with the highest coverage is drawn. 54 <help>By default the transcript isoform with the highest coverage is drawn.
54 Alternatively, the transcript isoform that is provided in the columns 55 Alternatively, the transcript isoform that is provided in the columns
55 transcript_id1 and transcript_id2 in the given fusions file can be drawn. 56 transcript_id1 and transcript_id2 in the given fusions file can be drawn.
56 Selecting the isoform with the highest coverage usually produces nicer plots, 57 Selecting the isoform with the highest coverage usually produces nicer plots,
79 <option value="none">none - only the fusion of interest is drawn</option> 80 <option value="none">none - only the fusion of interest is drawn</option>
80 <option value="low">low</option> 81 <option value="low">low</option>
81 <option value="medium">medium</option> 82 <option value="medium">medium</option>
82 <option value="high">high</option> 83 <option value="high">high</option>
83 </param> 84 </param>
84 <param argument="--showIntergenicVicinity" type="integer" value="" min="0" optional="true" label="Intergenic Vicinity">
85 <help>This option only applies to intergenic breakpoints.
86 If it is set to a value greater than 0, then the script draws the genes
87 which are no more than the given distance away from an intergenic breakpoint.
88 Note that this option is incompatible with squishIntrons.
89 Default: 0
90 </help>
91 </param>
92 <param argument="--squishIntrons" type="select" optional="true" label="Squish introns"> 85 <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
93 <help>Exons usually make up only a small fraction of a gene. 86 <help>Exons usually make up only a small fraction of a gene.
94 They may be hard to see in the plot. i 87 They may be hard to see in the plot. i
95 Since introns are in most situations of no interest in the context of gene fusions, 88 Since introns are in most situations of no interest in the context of gene fusions,
96 this switch can be used to shrink the size of introns to a fixed, negligible size. 89 this switch can be used to shrink the size of introns to a fixed, negligible size.
98 Default: TRUE 91 Default: TRUE
99 </help> 92 </help>
100 <option value="TRUE">True</option> 93 <option value="TRUE">True</option>
101 <option value="FALSE">False</option> 94 <option value="FALSE">False</option>
102 </param> 95 </param>
103 96 <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity">
97 <help>This option only applies to intergenic breakpoints.
98 If it is set to a value greater than 0, then the script draws the genes
99 which are no more than the given distance away from an intergenic breakpoint.
100 The keywords closestGene and closestProteinCodingGene instruct the script
101 to dynamically determine the distance to the next (protein-coding) gene for each breakpoint.
102 Alternatively, instead of specifying a single distance
103 that is applied upstream and downstream of both breakpoints alike,
104 more fine-grained control over the region to be shown is possible by specifying four comma-separated values.
105 The first two values determine the region to the left and to the right of breakpoint 1;
106 the third and fourth values determine the region to the left and to the right of breakpoint 2.
107 Note that this option is incompatible with squishIntrons.
108 Default: 0
109 </help>
110 <option value="closestGene">closestGene</option>
111 <option value="closestProteinCodingGene">closestProteinCodingGene</option>
112 <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$</validator>
113 </param>
104 <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By"> 114 <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
105 <help>Occasionally, domains are annotated redundantly. 115 <help>Occasionally, domains are annotated redundantly.
106 For example, tyrosine kinase domains are frequently annotated as 116 For example, tyrosine kinase domains are frequently annotated as
107 Protein tyrosine kinase and Protein kinase domain. 117 Protein tyrosine kinase and Protein kinase domain.
108 In order to simplify the visualization, such domains can be merged into one, 118 In order to simplify the visualization, such domains can be merged into one,
149 help="Default: 11.692"/> 159 help="Default: 11.692"/>
150 <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches" 160 <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
151 help="Default: 8.267"/> 161 help="Default: 8.267"/>
152 <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text" 162 <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
153 help="Default: 1.0"/> 163 help="Default: 1.0"/>
164 <param argument="--fontFamily" type="text" value="" optional="true" label="Font to use for all labels in the plots.">
165 <help>Default: Helvetica
166 </help>
167 <option value="serif">serif</option>
168 <option value="sans">sans</option>
169 <option value="mono">mono</option>
170 <option value="AvantGarde">AvantGarde</option>
171 <option value="Bookman">Bookman</option>
172 <option value="Courier">Courier</option>
173 <option value="Helvetica">Helvetica</option>
174 <option value="Helvetica-Narrow">Helvetica-Narrow</option>
175 <option value="NewCenturySchoolbook">NewCenturySchoolbook</option>
176 <option value="Palatino">Palatino</option>
177 <option value="Times">Times</option>
178 <option value="URWGothic">URWGothic</option>
179 <option value="URWBookman">URWBookman</option>
180 <option value="NimbusMon">NimbusMon</option>
181 <option value="NimbusSan">NimbusSan</option>
182 <option value="URWHelvetica">URWHelvetica</option>
183 <option value="NimbusSanCond">NimbusSanCond</option>
184 <option value="CenturySch">CenturySch</option>
185 <option value="URWPalladio">URWPalladio</option>
186 <option value="NimbusRom">NimbusRom</option>
187 <option value="URWTimes">URWTimes</option>
188 <option value="ArialMT">ArialMT</option>
189 <option value="Japan1">Japan1</option>
190 <option value="Japan1HeiMin">Japan1HeiMin</option>
191 <option value="Japan1GothicBBB">Japan1GothicBBB</option>
192 <option value="Japan1Ryumin">Japan1Ryumin</option>
193 <option value="Korea1">Korea1</option>
194 <option value="Korea1deb">Korea1deb</option>
195 <option value="CNS1">CNS1</option>
196 <option value="GB1">GB1</option>
197 </param>
198 <param argument="--fixedScale" type="integer" value="" min="0" optional="true" label="Apply a fixed scale to all fusions">
199 <help>By default, transcripts are scaled automatically to fill the entire page.
200 This parameter enforces a fixed scale to be applied to all fusions,
201 which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable.
202 A common use case is the visualization of a gene that is found to be fused to multiple partners.
203 By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage
204 in a single plot one above the other with matching scales.
205 Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn,
206 or else dynamic scaling is applied, because display errors would occur otherwise.
207 The default value is 0, which means that no fixed scale should be used
208 and that the scale should be adapted dynamically for each fusion. Default: 0
209 </help>
210 </param>
211 <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot">
212 <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes.
213 The plots can be cropped at a fixed level by passing a non-zero value to this parameter.
214 When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level.
215 When two comma-separated values are given, the cutoffs can be specified independently for the two plots.
216 A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage)
217 and that the coverage plots of both genes should be on the same scale. This is the default behavior.
218 A value of 0,0 also indicates that no cropping should be applied,
219 but the coverage plots of the two genes have different scales:
220 each one is scaled individually to the peak coverage of the respective gene.
221 Default: 0
222 </help>
223 <validator type="regex" message="">^\d+(,\d+)?$</validator>
224 </param>
154 </section> 225 </section>
155 </xml> 226 </xml>
156 <token name="@DRAW_FUSIONS@"> 227 <token name="@DRAW_FUSIONS@">
157 draw_fusions.R 228 draw_fusions.R
158 --fusions='$fusions' 229 --fusions='$fusions'
170 --transcriptSelection=$visualization.options.transcriptSelection 241 --transcriptSelection=$visualization.options.transcriptSelection
171 #end if 242 #end if
172 #if $visualization.options.minConfidenceForCircosPlot 243 #if $visualization.options.minConfidenceForCircosPlot
173 --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot 244 --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
174 #end if 245 #end if
175 #if $visualization.options.showIntergenicVicinity
176 --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
177 #end if
178 #if $visualization.options.squishIntrons 246 #if $visualization.options.squishIntrons
179 --squishIntrons=$visualization.options.squishIntrons 247 --squishIntrons=$visualization.options.squishIntrons
248 #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity
249 --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
250 #end if
180 #end if 251 #end if
181 #if $visualization.options.mergeDomainsOverlappingBy 252 #if $visualization.options.mergeDomainsOverlappingBy
182 --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy 253 --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
183 #end if 254 #end if
255 #if $visualization.options.sampleName
256 --sampleName=$visualization.options.sampleName
257 #end if
184 #if $visualization.options.printExonLabels 258 #if $visualization.options.printExonLabels
185 --printExonLabels=$visualization.options.printExonLabels 259 --printExonLabels=$visualization.options.printExonLabels
186 #end if 260 #end if
261 #if $visualization.options.coverageRange
262 --coverageRange="$visualization.options.coverageRange"
263 #end if
187 #if $visualization.options.render3dEffect 264 #if $visualization.options.render3dEffect
188 --render3dEffect=$visualization.options.render3dEffect 265 --render3dEffect=$visualization.options.render3dEffect
189 #end if 266 #end if
190 #if $visualization.options.optimizeDomainColors 267 #if $visualization.options.optimizeDomainColors
191 --optimizeDomainColors=$visualization.options.optimizeDomainColors 268 --optimizeDomainColors=$visualization.options.optimizeDomainColors
200 --pdfWidth=$visualization.options.pdfWidth 277 --pdfWidth=$visualization.options.pdfWidth
201 #end if 278 #end if
202 #if $visualization.options.pdfHeight 279 #if $visualization.options.pdfHeight
203 --pdfHeight=$visualization.options.pdfHeight 280 --pdfHeight=$visualization.options.pdfHeight
204 #end if 281 #end if
282 # fontFamily
283 #if $visualization.options.fontFamily
284 --fontFamily=$visualization.options.fontFamily
285 #end if
205 #if $visualization.options.fontSize 286 #if $visualization.options.fontSize
206 --fontSize=$visualization.options.fontSize 287 --fontSize=$visualization.options.fontSize
207 #end if 288 #end if
208 </token> 289 </token>
209 </macros> 290 </macros>