Mercurial > repos > iuc > drep_dereplicate
comparison macros.xml @ 3:a0713a10c9f6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 91d5bae878afa54d8264c1ca89c79b2d26ef35ad
author | iuc |
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date | Wed, 15 Mar 2023 11:05:04 +0000 |
parents | 368cb4bef9d8 |
children | 1faea6e8c92b |
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2:368cb4bef9d8 | 3:a0713a10c9f6 |
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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: |