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comparison macros.xml @ 11:2f09a07c94ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
author iuc
date Sat, 01 Oct 2022 08:42:18 +0000
parents 5f9a41f84844
children ca69a2c9afc9
comparison
equal deleted inserted replaced
10:5f9a41f84844 11:2f09a07c94ab
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.6</token> 2 <token name="@TOOL_VERSION@">3.7</token>
3 <token name="@VERSION_SUFFIX@">1</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@">pygenometracks</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement>
7 <yield /> 7 <yield />
8 </requirements> 8 </requirements>
58 <xml name="track_input_bedgraph_matrix_macro"> 58 <xml name="track_input_bedgraph_matrix_macro">
59 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/> 59 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/>
60 </xml> 60 </xml>
61 <xml name="track_input_link_macro"> 61 <xml name="track_input_link_macro">
62 <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/> 62 <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/>
63 </xml>
64 <xml name="track_input_fasta_macro">
65 <conditional name="fasta_source">
66 <param name="fasta_source_selector" type="select" label="Choose the source for the fasta to display">
67 <option value="cached">Locally cached</option>
68 <option value="history">History</option>
69 </param>
70 <when value="cached">
71 <param name="fasta_cached" type="select" label="Fasta availables">
72 <options from_data_table="fasta_indexes">
73 <validator type="no_options" message="No cached fasta is available"/>
74 </options>
75 </param>
76 </when>
77 <when value="history">
78 <param name="fasta_local" type="data" format="fasta" label="Fasta from history"/>
79 </when>
80 </conditional>
81 </xml>
82 <xml name="track_input_maf_macro">
83 <param name="track_input_maf" type="data" format="maf" label="Track file for maf" multiple="False"/>
63 </xml> 84 </xml>
64 <!-- Common to nearly all tracks: --> 85 <!-- Common to nearly all tracks: -->
65 <xml name="plot_title"> 86 <xml name="plot_title">
66 <param name="title" type="text" optional="true" label="Plot title" multiple="True"/> 87 <param name="title" type="text" optional="true" label="Plot title" multiple="True"/>
67 </xml> 88 </xml>
164 </when> 185 </when>
165 <when value="bed_rgb" /> 186 <when value="bed_rgb" />
166 <when value="none" /> 187 <when value="none" />
167 </conditional> 188 </conditional>
168 </xml> 189 </xml>
190 <xml name="backbone_color_bed_macro">
191 <conditional name="backbone_color_bed">
192 <param name="backbone_color_bed_select" type="select" label="Define the color of the backbone:">
193 <option value="manually" selected="True">manually</option>
194 <option value="bed_rgb">From the 9th field</option>
195 <option value="none">No border</option>
196 </param>
197 <when value="manually">
198 <param name="color" type="color" value="#000000" label="Color of the backbone"/>
199 </when>
200 <when value="bed_rgb" />
201 <when value="none" />
202 </conditional>
203 </xml>
169 <xml name="bed_advanced_macro"> 204 <xml name="bed_advanced_macro">
170 <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false" 205 <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false"
171 label="Global max rows" /> 206 label="Global max rows" />
172 <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" /> 207 <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" />
173 <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" /> 208 <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" />
174 <param name="line_width" type="float" value="0.5" label="width of lines" /> 209 <param name="line_width" type="float" value="0.5" label="width of lines" />
175 <section name ="gtf" title="When using gtf as input" expanded="False"> 210 <section name ="gtf" title="When using gtf as input" expanded="False">
176 <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label" 211 <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
177 help="Usually transcript_name or gene_name"/> 212 help="Usually transcript_name or gene_name"/>
178 <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false" 213 <conditional name="merge_transcripts">
179 label="Merge all transcripts of each gene in a single entry" /> 214 <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry">
215 <option value="false" selected="True">No</option>
216 <option value="true">Yes</option>
217 </param>
218 <when value="true">
219 <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true"
220 label="Merge overlapping exons" help="Usually it makes prettier plots" />
221 </when>
222 <when value="false" />
223 </conditional>
180 </section> 224 </section>
181 </xml> 225 </xml>
182 <xml name="utr_macro"> 226 <xml name="utr_macro">
183 <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/> 227 <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/>
184 <conditional name="color_utr"> 228 <conditional name="color_utr">
350 <option value="plasma_r">plasma reversed</option> 394 <option value="plasma_r">plasma reversed</option>
351 <option value="inferno_r">inferno reversed</option> 395 <option value="inferno_r">inferno reversed</option>
352 <option value="magma_r">magma reversed</option> 396 <option value="magma_r">magma reversed</option>
353 <option value="cividis_r">cividis reversed</option> 397 <option value="cividis_r">cividis reversed</option>
354 </xml> 398 </xml>
399 <xml name="links_arcs_triangles_options">
400 <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:">
401 <option value="0" selected="True">default (proportional to distance)</option>
402 <option value="1">compacted (the height is proportional to the square root of the distance)</option>
403 <option value="2">highly compacted (the height is the same for all distances)</option>
404 </param>
405 <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops">
406 <option value="false" selected="True">Extremities (start of first and end of second)</option>
407 <option value="true">Center (mean of start and end for each)</option>
408 </param>
409 </xml>
410 <xml name="region2_option">
411 <param name="region2" type="text" label="Region of the genome that should be plotted on the y axis" optional="true"
412 value="" help="The format is chr:start-end, for example chr10:10-500. By default this is the region on the x-axis. Top is start and bottom is end. Use 'Invert the track' if you want the contrary.">
413 <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator>
414 </param>
415 </xml>
355 </macros> 416 </macros>