Mercurial > repos > iuc > semibin_concatenate_fasta

comparison macros.xml @ 5:2c7ed948eeed draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
author iuc
date Sun, 10 Aug 2025 11:38:22 +0000
parents c72b50829c03
children a72b974c98a2
comparison
equal deleted inserted replaced
4:c72b50829c03 5:2c7ed948eeed
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">2.0.2</token> 3 <token name="@TOOL_VERSION@">2.1.0</token>
4 <token name="@VERSION_SUFFIX@">2</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">24.0</token> 5 <token name="@PROFILE@">21.01</token>
6 <xml name="biotools"> 6 <xml name="biotools">
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">semibin</xref> 8 <xref type="bio.tools">semibin</xref>
9 </xrefs> 9 </xrefs>
10 </xml> 10 </xml>
46 <when value="multi"> 46 <when value="multi">
47 <expand macro="input-fasta-multi"/> 47 <expand macro="input-fasta-multi"/>
48 </when> 48 </when>
49 </conditional> 49 </conditional>
50 </xml> 50 </xml>
51 <xml name="mode_fasta_strobealign">
52 <conditional name="mode">
53 <expand macro="mode_select"/>
54 <when value="single">
55 <expand macro="input-fasta-single"/>
56 <expand macro="input-txt"/>
57 </when>
58 <when value="co">
59 <expand macro="input-fasta-single"/>
60 <expand macro="input-txt"/>
61 </when>
62 <when value="multi">
63 <expand macro="input-fasta-multi"/>
64 <expand macro="input-txt"/>
65 </when>
66 </conditional>
67 </xml>
51 <xml name="mode_select"> 68 <xml name="mode_select">
52 <param name="select" type="select" label="Binning mode"> 69 <param name="select" type="select" label="Binning mode">
53 <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option> 70 <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option>
54 <option value="co">Co-assembly binning (samples are co-assembled together and binned together)</option> 71 <option value="co">Co-assembly binning (samples are co-assembled together and binned together)</option>
55 <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option> 72 <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option>
73 </param>
74 </xml>
75 <xml name="bam_or_strobealign">
76 <param name="align_select" type="select" label="Use bam or strobealign abundance files?" help="Strobealign abundance files can only be used when samples used in binning above or equal 5">
77 <option value="bam">BAM</option>
78 <option value="txt">Strobealign-aemb file(s)</option>
56 </param> 79 </param>
57 </xml> 80 </xml>
58 <xml name="input-fasta-single"> 81 <xml name="input-fasta-single">
59 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/> 82 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>
60 </xml> 83 </xml>
127 <param argument="--input-bam" type="data" format="bam" label="Read mapping to the contigs" help="Sorted BAM files"/> 150 <param argument="--input-bam" type="data" format="bam" label="Read mapping to the contigs" help="Sorted BAM files"/>
128 </xml> 151 </xml>
129 <xml name="input-bam-multi"> 152 <xml name="input-bam-multi">
130 <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/> 153 <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/>
131 </xml> 154 </xml>
155 <!-- Strobealign files -->
156 <xml name="input-txt">
157 <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/>
158 </xml>
132 <token name="@BAM_FILES@"><![CDATA[ 159 <token name="@BAM_FILES@"><![CDATA[
133 #if $mode.select == 'single' 160 #if $mode.select == 'single'
134 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_bam.element_identifier)) 161 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.input_bam.element_identifier))
135 ln -s '$input_bam' '${identifier}.bam' && 162 ln -s '$mode.input_bam' '${identifier}.bam' &&
136 #else 163 #else
137 #for $e in $input_bam 164 #for $e in $mode.input_bam
138 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) 165 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
139 ln -s '$e' '${identifier}.bam' && 166 ln -s '$e' '${identifier}.bam' &&
140 #end for 167 #end for
141 #end if 168 #end if
169 ]]></token>
170 <token name="@STROBEALIGN_FILES@"><![CDATA[
171 #for $e in $mode.align_select.abundance
172 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
173 ln -s '$e' '${identifier}.txt' &&
174 #end for
142 ]]></token> 175 ]]></token>
143 <xml name="ref_select_cannot"> 176 <xml name="ref_select_cannot">
144 <param name="select" type="select" label="Reference database"> 177 <param name="select" type="select" label="Reference database">
145 <option value="cached">Cached database</option> 178 <option value="cached">Cached database</option>
146 <option value="taxonomy">Pre-computed taxonomy</option> 179 <option value="taxonomy">Pre-computed taxonomy</option>
255 </xml> 288 </xml>
256 <xml name="orf-finder"> 289 <xml name="orf-finder">
257 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins"> 290 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
258 <option value="fast-naive" selected="true">Fast-Naive</option> 291 <option value="fast-naive" selected="true">Fast-Naive</option>
259 <option value="prodigal">Prodigal</option> 292 <option value="prodigal">Prodigal</option>
260 <option value="fraggenescan">Fraggenescan</option>
261 </param> 293 </param>
262 </xml> 294 </xml>
263 <xml name="max-node"> 295 <xml name="max-node">
264 <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/> 296 <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/>
265 </xml> 297 </xml>
291 <xml name="data"> 323 <xml name="data">
292 <param argument="--data" type="data" format="csv" label="Train data"/> 324 <param argument="--data" type="data" format="csv" label="Train data"/>
293 </xml> 325 </xml>
294 <xml name="data_output_single"> 326 <xml name="data_output_single">
295 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data"> 327 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
296 <filter>mode["select"]=="single" or mode["select"]=="co"</filter> 328 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
297 </data> 329 </data>
298 <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data"> 330 <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
299 <filter>mode["select"]=="single" or mode["select"]=="co"</filter> 331 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
300 </data> 332 </data>
301 </xml> 333 </xml>
302 <xml name="data_output_multi"> 334 <xml name="data_output_multi">
303 <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample"> 335 <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
304 <filter>mode["select"]=="multi"</filter> 336 <filter>input_type_select['mode']['select']=="multi"</filter>
305 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> 337 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
306 </collection> 338 </collection>
307 <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample"> 339 <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
308 <filter>mode["select"]=="multi"</filter> 340 <filter>input_type_select['mode']['select']=="multi"</filter>
309 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> 341 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
310 </collection> 342 </collection>
311 </xml> 343 </xml>
312 <xml name="generate_sequence_features_extra_outputs"> 344 <xml name="generate_sequence_features_extra_outputs">
313 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage"> 345 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
314 <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> 346 <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
347 <filter>input_type_select['input_type']=="bam"</filter>
315 </data> 348 </data>
316 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)"> 349 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
317 <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> 350 <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
351 <filter>input_type_select['input_type']=="bam"</filter>
318 </data> 352 </data>
319 <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)"> 353 <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
320 <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> 354 <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
355 <filter>input_type_select['input_type']=="bam"</filter>
321 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" /> 356 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
322 </collection> 357 </collection>
323 <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> 358 <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
324 <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> 359 <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
360 <filter>input_type_select['input_type']=="bam"</filter>
325 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" /> 361 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
326 </collection> 362 </collection>
363 <data name="cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
364 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
365 <filter>input_type_select['input_type']=="txt"</filter>
366 </data>
367 <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
368 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
369 <filter>input_type_select['input_type']=="txt"</filter>
370 </data>
371 <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
372 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
373 <filter>input_type_select['input_type']=="txt"</filter>
374 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
375 </collection>
327 <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)"> 376 <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
328 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> 377 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
378 <filter>input_type_select['input_type']=="bam"</filter>
379 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" recurse="true"/>
380 </collection>
381 <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
382 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
383 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
384 </collection>
385 <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
386 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
387 <filter>input_type_select['input_type']=="bam"</filter>
388 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
389 </collection>
390 <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
391 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
392 <filter>input_type_select['input_type']=="bam"</filter>
393 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" match_relative_path="true" recurse="true"/>
394 </collection>
395 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
396 <filter>input_type_select['mode']['select']=="multi" and extra_output and "contigs" in extra_output</filter>
397 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
398 </collection>
399 </xml>
400 <xml name="generate_sequence_features_extra_outputs_main">
401 <!-- Single -->
402 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
403 <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
404 </data>
405 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
406 <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
407 </data>
408 <!-- Bam co aligned -->
409 <collection name="co_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
410 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
411 <filter>mode['align_select']</filter>
412 <filter>mode['align_select']['align_select']=="bam"</filter>
413 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
414 </collection>
415 <collection name="co_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
416 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
417 <filter>mode['align_select']</filter>
418 <filter>mode['align_select']['align_select']=="bam"</filter>
419 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
420 </collection>
421
422 <!-- Bam Multi aligned -->
423 <collection name="multi_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
424 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
425 <filter>mode['align_select']</filter>
426 <filter>mode['align_select']['align_select']=="bam"</filter>
329 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" /> 427 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
330 </collection> 428 </collection>
331 <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample"> 429 <collection name="multi_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
332 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> 430 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
431 <filter>mode['align_select']</filter>
432 <filter>mode['align_select']['align_select']=="bam"</filter>
333 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> 433 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
334 </collection> 434 </collection>
335 <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)"> 435 <collection name="multi_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
336 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> 436 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
437 <filter>mode['align_select']</filter>
438 <filter>mode['align_select']['align_select']=="bam"</filter>
337 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" /> 439 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
338 </collection> 440 </collection>
339 <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)"> 441 <collection name="multi_split_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
340 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> 442 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
443 <filter>mode['align_select']</filter>
444 <filter>mode['align_select']['align_select']=="bam"</filter>
445 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
446 </collection>
447 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
448 <filter>mode['select']=="multi" and extra_output and "contigs" in extra_output</filter>
449 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
450 </collection>
451 <!-- Txt co aligned -->
452 <data name="co_split_cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
453 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
454 <filter>mode['align_select']</filter>
455 <filter>mode['align_select']['align_select']=="txt"</filter>
456 </data>
457 <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
458 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
459 <filter>mode['align_select']</filter>
460 <filter>mode['align_select']['align_select']=="txt"</filter>
461 </data>
462 <!-- Txt multi aligned -->
463 <collection name="multi_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage per sample (aemb)">
464 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
465 <filter>mode['align_select']</filter>
466 <filter>mode['align_select']['align_select'] =="txt"</filter>
467 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
468 </collection>
469 <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
470 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
471 <filter>mode['align_select']</filter>
472 <filter>mode['align_select']['align_select']=="txt"</filter>
341 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> 473 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
342 </collection> 474 </collection>
343 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
344 <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
345 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
346 </collection>
347
348 </xml> 475 </xml>
349 <xml name="train_output"> 476 <xml name="train_output">
350 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" /> 477 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
351 </xml> 478 </xml>
352 <xml name="cannot_link_output"> 479 <xml name="cannot_link_output">
353 <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" /> 480 <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" />
354 </xml> 481 </xml>
355 <token name="@HELP_HEADER@"><![CDATA[ 482 <token name="@HELP_HEADER@"><![CDATA[
483
356 What it does 484 What it does
357 ============ 485 ============
358 486
359 SemiBin is a Semi-supervised siamese neural network for metagenomic binning 487 SemiBin is a Semi-supervised siamese neural network for metagenomic binning
360 488 ]]></token>
361 ]]></token>
362 <token name="@HELP_INPUT_FASTA@"><![CDATA[ 489 <token name="@HELP_INPUT_FASTA@"><![CDATA[
363 - Contigs in fasta for 1 or several samples from single or co-assembly 490 - Contigs in fasta for 1 or several samples from single or co-assembly
364 ]]></token> 491 ]]></token>
365 <token name="@HELP_INPUT_BAM@"><![CDATA[ 492 <token name="@HELP_INPUT_BAM@"><![CDATA[
366 - BAM with reads mapping to the contigs 493 - BAM with reads mapping to the contigs
367 ]]></token> 494 ]]></token>
495 <token name="@HELP_INPUT_STROBEALIGN@"><![CDATA[
496 - TXT alignment files that are the output of strobealign-aemb
497 ]]></token>
368 <token name="@HELP_CANNOT@"><![CDATA[ 498 <token name="@HELP_CANNOT@"><![CDATA[
369 - Cannot-link constraints 499 - Cannot-link constraints
370 ]]></token> 500 ]]></token>
371 <token name="@HELP_DATA@"><![CDATA[ 501 <token name="@HELP_DATA@"><![CDATA[
372 - Training data and split training data for the model 502 - Training data and split training data for the model
373 ]]></token> 503 ]]></token>
374 <token name="@HELP_MODEL@"><![CDATA[ 504 <token name="@HELP_MODEL@"><![CDATA[
375 - Semi-supervised deep learning model 505 - Semi-supervised deep learning model
376 ]]></token> 506 ]]></token>
377 <token name="@HELP_BINS@"><![CDATA[ 507 <token name="@HELP_BINS@"><![CDATA[
378 - Reconstructed bins after reclustering 508 - Reconstructed bins after reclustering
379 - Reconstructed bins before reclustering 509 - Reconstructed bins before reclustering
380 ]]></token> 510 ]]></token>
381 <xml name="citations"> 511 <xml name="citations">
382 <citations> 512 <citations>
383 <citation type="doi">10.1038/s41467-022-29843-y</citation> 513 <citation type="doi">10.1038/s41467-022-29843-y</citation>
384 </citations> 514 </citations>
385 </xml> 515 </xml>