Mercurial > repos > jjohnson > arriba_download_reference
comparison macros.xml @ 0:7345cb1bb772 draft
"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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| -1:000000000000 | 0:7345cb1bb772 |
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| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">2.2.1</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="Arriba Genome assembly and annotation source"> | |
| 22 <option value="history">From your history</option> | |
| 23 <option value="cached">Use built-in Arriba</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 <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/> | |
| 28 </when> | |
| 29 <when value="cached"> | |
| 30 <param name="arriba_ref" type="select" label="Arriba Genome assembly and annotation"> | |
| 31 <options from_data_table="arriba_indexes"> | |
| 32 </options> | |
| 33 </param> | |
| 34 </when> | |
| 35 </conditional> | |
| 36 </xml> | |
| 37 <token name="@GENOME_SOURCE@"> | |
| 38 #if str($genome.genome_source) == "history" | |
| 39 #if $genome.assembly | |
| 40 #set $genome_assembly = $genome.assembly | |
| 41 #end if | |
| 42 #set $genome_annotation = $genome.annotation | |
| 43 #else | |
| 44 #set $genome_assembly = $genome.arriba_ref.fields.fasta | |
| 45 #set $genome_annotation = $genome.arriba_ref.fields.gtf | |
| 46 #end if | |
| 47 </token> | |
| 48 | |
| 49 <xml name="visualization_options"> | |
| 50 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> | |
| 51 <section name="options" expanded="false" title="Draw Fusion Options"> | |
| 52 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection"> | |
| 53 <help>By default the transcript isoform with the highest coverage is drawn. | |
| 54 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 Selecting the isoform with the highest coverage usually produces nicer plots, | |
| 57 in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint. | |
| 58 However, the isoform with the highest coverage may not be the one that is involved in the fusion. | |
| 59 Often, genomic rearrangements lead to non-canonical isoforms being transcribed. | |
| 60 For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2, | |
| 61 which reflect the actual isoforms involved in a fusion. | |
| 62 \ As a third option, the transcripts that are annotated as canonical can be drawn. | |
| 63 Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical. | |
| 64 </help> | |
| 65 <option value="coverage">coverage</option> | |
| 66 <option value="provided">provided</option> | |
| 67 <option value="canonical">canonical</option> | |
| 68 </param> | |
| 69 <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection"> | |
| 70 <help>The fusion of interest is drawn as a solid line in the circos plot. | |
| 71 To give an impression of the overall degree of rearrangement, | |
| 72 all other fusions are drawn as semi-transparent lines in the background. | |
| 73 This option determines which other fusions should be included in the circos plot. | |
| 74 Values specify the minimum confidence a fusion must have to be included. | |
| 75 It usually makes no sense to include low-confidence fusions in circos plots, | |
| 76 because they are abundant and unreliable, and would clutter up the circos plot. | |
| 77 Default: medium | |
| 78 </help> | |
| 79 <option value="none">none - only the fusion of interest is drawn</option> | |
| 80 <option value="low">low</option> | |
| 81 <option value="medium">medium</option> | |
| 82 <option value="high">high</option> | |
| 83 </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"> | |
| 93 <help>Exons usually make up only a small fraction of a gene. | |
| 94 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, | |
| 96 this switch can be used to shrink the size of introns to a fixed, negligible size. | |
| 97 It makes sense to disable this feature, if breakpoints in introns are of importance. | |
| 98 Default: TRUE | |
| 99 </help> | |
| 100 <option value="TRUE">True</option> | |
| 101 <option value="FALSE">False</option> | |
| 102 </param> | |
| 103 | |
| 104 <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. | |
| 106 For example, tyrosine kinase domains are frequently annotated as | |
| 107 Protein tyrosine kinase and Protein kinase domain. | |
| 108 In order to simplify the visualization, such domains can be merged into one, | |
| 109 given that they overlap by the given fraction. | |
| 110 The description of the larger domain is used. | |
| 111 Default: 0.9 | |
| 112 </help> | |
| 113 </param> | |
| 114 <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels"> | |
| 115 <help>By default the number of an exon is printed inside each exon, | |
| 116 which is taken from the attribute exon_number of the GTF annotation. | |
| 117 When a gene has many exons, the boxes may be too narrow to contain the labels, | |
| 118 resulting in unreadable exon labels. In these situations, i | |
| 119 it may be better to turn off exon labels. | |
| 120 Default: TRUE | |
| 121 </help> | |
| 122 <option value="TRUE">True</option> | |
| 123 <option value="FALSE">False</option> | |
| 124 </param> | |
| 125 <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect"> | |
| 126 <help>Whether light and shadow should be rendered to give objects a 3D effect. | |
| 127 Default: TRUE | |
| 128 </help> | |
| 129 <option value="TRUE">True</option> | |
| 130 <option value="FALSE">False</option> | |
| 131 </param> | |
| 132 <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors"> | |
| 133 <help>By default, the script colorizes domains according to the colors | |
| 134 specified in the file given in --annotation. | |
| 135 This way, coloring of domains is consistent across all proteins. | |
| 136 But since there are more distinct domains than colors, | |
| 137 this can lead to different domains having the same color. | |
| 138 If this option is set to TRUE, the colors are recomputed for each fusion separately. | |
| 139 This ensures that the colors have the maximum distance for each individual fusion, | |
| 140 but they are no longer consistent across different fusions. | |
| 141 Default: FALSE | |
| 142 </help> | |
| 143 <option value="TRUE">True</option> | |
| 144 <option value="FALSE">False</option> | |
| 145 </param> | |
| 146 <param argument="--color1" type="color" value="" optional="true" label="Color of the 5' end of the fusion."/> | |
| 147 <param argument="--color2" type="color" value="" optional="true" label="Color of the 3' end of the fusion."/> | |
| 148 <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches" | |
| 149 help="Default: 11.692"/> | |
| 150 <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches" | |
| 151 help="Default: 8.267"/> | |
| 152 <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text" | |
| 153 help="Default: 1.0"/> | |
| 154 </section> | |
| 155 </xml> | |
| 156 <token name="@DRAW_FUSIONS@"> | |
| 157 draw_fusions.R | |
| 158 --fusions='$fusions' | |
| 159 --alignments='Aligned.sortedByCoord.out.bam' | |
| 160 --annotation='$genome.annotation' | |
| 161 --output=fusions.pdf | |
| 162 #if $visualization.cytobands | |
| 163 --cytobands='$visualization.cytobands' | |
| 164 #end if | |
| 165 #if $protein_domains | |
| 166 --proteinDomains='$protein_domains' | |
| 167 #end if | |
| 168 ## Visualization Options | |
| 169 #if $visualization.options.transcriptSelection | |
| 170 --transcriptSelection=$visualization.options.transcriptSelection | |
| 171 #end if | |
| 172 #if $visualization.options.minConfidenceForCircosPlot | |
| 173 --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot | |
| 174 #end if | |
| 175 #if $visualization.options.showIntergenicVicinity | |
| 176 --showIntergenicVicinity=$visualization.options.showIntergenicVicinity | |
| 177 #end if | |
| 178 #if $visualization.options.squishIntrons | |
| 179 --squishIntrons=$visualization.options.squishIntrons | |
| 180 #end if | |
| 181 #if $visualization.options.mergeDomainsOverlappingBy | |
| 182 --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy | |
| 183 #end if | |
| 184 #if $visualization.options.printExonLabels | |
| 185 --printExonLabels=$visualization.options.printExonLabels | |
| 186 #end if | |
| 187 #if $visualization.options.render3dEffect | |
| 188 --render3dEffect=$visualization.options.render3dEffect | |
| 189 #end if | |
| 190 #if $visualization.options.optimizeDomainColors | |
| 191 --optimizeDomainColors=$visualization.options.optimizeDomainColors | |
| 192 #end if | |
| 193 #if $visualization.options.color1 | |
| 194 --color1=$visualization.options.color1 | |
| 195 #end if | |
| 196 #if $visualization.options.color2 | |
| 197 --color2=$visualization.options.color2 | |
| 198 #end if | |
| 199 #if $visualization.options.pdfWidth | |
| 200 --pdfWidth=$visualization.options.pdfWidth | |
| 201 #end if | |
| 202 #if $visualization.options.pdfHeight | |
| 203 --pdfHeight=$visualization.options.pdfHeight | |
| 204 #end if | |
| 205 #if $visualization.options.fontSize | |
| 206 --fontSize=$visualization.options.fontSize | |
| 207 #end if | |
| 208 </token> | |
| 209 </macros> |