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comparison macros.xml @ 11:f0334664a47b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 802d7fe606623d900fd0d5de157e87166c0b7e84
author iuc
date Wed, 07 May 2025 11:01:52 +0000
parents 30d4702cdba6
children
comparison
equal deleted inserted replaced
10:30d4702cdba6 11:f0334664a47b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">3.6.2</token> 3 <token name="@TOOL_VERSION@">3.6.2</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</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>
9 </xrefs> 9 </xrefs>
334 <option value="warnings" selected="true">Warnings</option> 334 <option value="warnings" selected="true">Warnings</option>
335 <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option> 335 <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option>
336 <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option> 336 <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option>
337 <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option> 337 <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option>
338 <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option> 338 <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option>
339 <option value="Bdb">Bdb.csv Basic genome statistics</option>
340 <option value="Cdb">Cdb.csv Clustering results</option>
341 <option value="Mdb">Mdb.csv Mash distance matrix</option>
342 <option value="Ndb">Ndb.csv ANI results between representative genomes</option>
343 <!-- Tdb
344 Taxonomy (as determined by centrifuge)
345 Sdb
346 The score of each genome
347 Wdb
348 The cluster and score of de-replicated genomes -->
339 <yield/> 349 <yield/>
340 </param> 350 </param>
341 </xml> 351 </xml>
342 <xml name="select_drep_outputs"> 352 <xml name="select_drep_outputs">
343 <expand macro="select_outputs"> 353 <expand macro="select_outputs">
344 <option value="Cluster_scoring">Cluster_scoring.pdf</option> 354 <option value="Cluster_scoring">Cluster_scoring.pdf</option>
345 <option value="Winning_genomes">Winning_genomes.pdf</option> 355 <option value="Winning_genomes">Winning_genomes.pdf</option>
346 <option value="Widb">Widb.csv</option> 356 <option value="Widb">Widb.csv CheckM information on de-replicated genomes</option>
347 <option value="Chdb">Chdb.tsv</option> 357 <option value="Chdb">Chdb.tsv CheckM results for all genomes</option>
348 </expand> 358 </expand>
349 </xml> 359 </xml>
350 <xml name="test_default_select_drep_outputs"> 360 <xml name="test_default_select_drep_outputs">
351 <param name="select_outputs" value="log,warnings,Primary_clustering_dendrogram,Clustering_scatterplots,Cluster_scoring,Winning_genomes,Widb" /> 361 <param name="select_outputs" value="log,warnings,Primary_clustering_dendrogram,Clustering_scatterplots,Cluster_scoring,Winning_genomes,Widb" />
352 </xml> 362 </xml>
370 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf"> 380 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf">
371 <filter>'Secondary_clustering_MDS' in select_outputs</filter> 381 <filter>'Secondary_clustering_MDS' in select_outputs</filter>
372 </data> 382 </data>
373 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf"> 383 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf">
374 <filter>'Clustering_scatterplots' in select_outputs</filter> 384 <filter>'Clustering_scatterplots' in select_outputs</filter>
385 </data>
386 <data name="Bdb" format="csv" label="${tool.name} on ${on_string}: Bdb Basic genome statistics" from_work_dir="outdir/data_tables/Bdb.csv">
387 <filter>'' in select_outputs</filter>
388 </data>
389 <data name="Cdb" format="csv" label="${tool.name} on ${on_string}: Cdb Clustering results" from_work_dir="outdir/data_tables/Cdb.csv">
390 <filter>'Cdb' in select_outputs</filter>
391 </data>
392 <data name="Mdb" format="csv" label="${tool.name} on ${on_string}: Mdb Mash distance matrix" from_work_dir="outdir/data_tables/Mdb.csv">
393 <filter>'' in select_outputs</filter>
394 </data>
395 <data name="Ndb" format="csv" label="${tool.name} on ${on_string}: Ndb ANI results between representative genomes" from_work_dir="outdir/data_tables/Ndb.csv">
396 <filter>'Ndb' in select_outputs</filter>
375 </data> 397 </data>
376 </xml> 398 </xml>
377 <xml name="drep_outputs"> 399 <xml name="drep_outputs">
378 <expand macro="common_outputs"/> 400 <expand macro="common_outputs"/>
379 <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf"> 401 <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf">