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comparison macros.xml @ 4:8a5ddbd5895f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 91d5bae878afa54d8264c1ca89c79b2d26ef35ad
author iuc
date Wed, 15 Mar 2023 11:04:06 +0000
parents 5482fd8d4418
children 7c08baa42fc8
comparison
equal deleted inserted replaced
3:5482fd8d4418 4:8a5ddbd5895f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">3.3.0</token> 3 <token name="@TOOL_VERSION@">3.4.2</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">20.01</token> 5 <token name="@PROFILE@">20.01</token>
6 <xml name="biotools"> 6 <xml name="biotools">
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">drep</xref> 8 <xref type="bio.tools">drep</xref>
269 <param argument="--contamination_weight" type="float" value="5" label="Contamination weight"/> 269 <param argument="--contamination_weight" type="float" value="5" label="Contamination weight"/>
270 <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="Strain heterogeneity weight"/> 270 <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="Strain heterogeneity weight"/>
271 <param argument="--N50_weight" type="float" value=".5" label="Weight of log(genome N50)"/> 271 <param argument="--N50_weight" type="float" value=".5" label="Weight of log(genome N50)"/>
272 <param argument="--size_weight" type="float" value="0" label="Weight of log(genome size)"/> 272 <param argument="--size_weight" type="float" value="0" label="Weight of log(genome size)"/>
273 <param argument="--centrality_weight" type="float" value="1" label="Weight of (centrality - S_ani)"/> 273 <param argument="--centrality_weight" type="float" value="1" label="Weight of (centrality - S_ani)"/>
274 <param argument="--extra_weight_table" type="data" format="tabular" multiple="false" optional="true" label="Genome specific extra weight"/>
274 </section> 275 </section>
275 </xml> 276 </xml>
276 <xml name="test_default_scoring_options"> 277 <xml name="test_default_scoring_options">
277 <section name="scoring"> 278 <section name="scoring">
278 <param name="completeness_weight" value="1"/> 279 <param name="completeness_weight" value="1"/>
281 <param name="N50_weight" value=".5" /> 282 <param name="N50_weight" value=".5" />
282 <param name="size_weight" value="0"/> 283 <param name="size_weight" value="0"/>
283 <param name="centrality_weight" value="1"/> 284 <param name="centrality_weight" value="1"/>
284 </section> 285 </section>
285 </xml> 286 </xml>
287 <xml name="test_extra_weight_table_scoring_options">
288 <section name="scoring">
289 <param name="completeness_weight" value="1"/>
290 <param name="contamination_weight" value="5"/>
291 <param name="strain_heterogeneity_weight" value="1"/>
292 <param name="N50_weight" value=".5" />
293 <param name="size_weight" value="0"/>
294 <param name="centrality_weight" value="1"/>
295 <param name="extra_weight_table" ftype="tabular" value="extra_weight_table_test"/>
296 </section>
297 </xml>
286 <token name="@SCORING_OPTIONS@"><![CDATA[ 298 <token name="@SCORING_OPTIONS@"><![CDATA[
287 --completeness_weight $scoring.completeness_weight 299 --completeness_weight $scoring.completeness_weight
288 --contamination_weight $scoring.contamination_weight 300 --contamination_weight $scoring.contamination_weight
289 --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight 301 --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight
290 --N50_weight $scoring.N50_weight 302 --N50_weight $scoring.N50_weight
291 --size_weight $scoring.size_weight 303 --size_weight $scoring.size_weight
292 --centrality_weight $scoring.centrality_weight 304 --centrality_weight $scoring.centrality_weight
305 #if str($extra_weight_table) != 'None'
306 --extra_weight_table $extra_weight_table
307 #end if
308
293 ]]></token> 309 ]]></token>
294 310
295 <xml name="warning_options"> 311 <xml name="warning_options">
296 <section name="warning" title="Warnings" expanded="false"> 312 <section name="warning" title="Warnings" expanded="false">
297 <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="How far from the threshold to throw cluster warnings"/> 313 <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="How far from the threshold to throw cluster warnings"/>
481 strain heterogeneity weight (default: 1) 497 strain heterogeneity weight (default: 1)
482 -N50W N50_WEIGHT, --N50_weight N50_WEIGHT 498 -N50W N50_WEIGHT, --N50_weight N50_WEIGHT
483 weight of log(genome N50) (default: 0.5) 499 weight of log(genome N50) (default: 0.5)
484 -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT 500 -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
485 weight of log(genome size) (default: 0) 501 weight of log(genome size) (default: 0)
502 -extraW EXTRA_WEIGHT_TABLE, --extra_weight_table EXTRA_WEIGHT_TABLE
503 Path to a tab-separated file with two-columns, no headers, listing genome and extra score to apply to that genome (optional)
486 504
487 505
488 ]]></token> 506 ]]></token>
489 <token name="@TAXONOMY_HELP@"><![CDATA[ 507 <token name="@TAXONOMY_HELP@"><![CDATA[
490 TAXONOMY: 508 TAXONOMY: