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comparison macros.xml @ 3:b55f0ce54d97 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
author iuc
date Tue, 28 Oct 2025 08:16:56 +0000
parents f5aff7c9a65d
children
comparison
equal deleted inserted replaced
2:f5aff7c9a65d 3:b55f0ce54d97
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@">1</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@PROFILE@">21.01</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>
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>
56 </param> 73 </param>
57 </xml> 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>
79 </param>
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,fasta.bz2" label="Contig sequences"/>
60 </xml> 83 </xml>
61 <xml name="input-fasta-multi"> 84 <xml name="input-fasta-multi">
62 <conditional name="multi_fasta"> 85 <conditional name="multi_fasta">
63 <param name="select" type="select" label="Contig files of the samples"> 86 <param name="select" type="select" label="Contig files of the samples">
64 <option value="concatenated" selected="true">1 concatenated file (created using the dedicated tool) with all sample contigs </option> 87 <option value="concatenated" selected="true">1 concatenated file (created using the dedicated tool) with all sample contigs </option>
65 <option value="multi">1 contig file per sample</option> 88 <option value="multi">1 contig file per sample</option>
66 </param> 89 </param>
67 <when value="concatenated"> 90 <when value="concatenated">
68 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Combined contig sequences"/> 91 <param argument="--input-fasta" type="data" format="fasta,fasta.gz,fasta.bz2" label="Combined contig sequences"/>
69 <expand macro="separator"/> 92 <expand macro="separator"/>
70 </when> 93 </when>
71 <when value="multi"> 94 <when value="multi">
72 <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/> 95 <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
73 <expand macro="concat_min_len"/> 96 <expand macro="concat_min_len"/>
74 </when> 97 </when>
75 </conditional> 98 </conditional>
76 </xml> 99 </xml>
77 <xml name="concat_min_len"> 100 <xml name="concat_min_len">
78 <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/> 101 <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/>
79 </xml> 102 </xml>
80 <token name="@SINGLE_FASTA_FILES@"><![CDATA[ 103 <token name="@SINGLE_FASTA_FILES@"><![CDATA[
81 #if $input_fasta.ext.endswith(".gz") 104 ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
82 gunzip -c '$input_fasta' > 'contigs.fasta' &&
83 #else
84 ln -s '$input_fasta' 'contigs.fasta' &&
85 #end if
86 ]]></token> 105 ]]></token>
87 <token name="@FASTA_FILES@"><![CDATA[ 106 <token name="@FASTA_FILES@"><![CDATA[
88 #if $mode.select == 'single' or $mode.select == 'co' 107 #if $mode.select == 'single' or $mode.select == 'co'
89 #if $mode.input_fasta.ext.endswith(".gz") 108 ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
90 gunzip -c '$mode.input_fasta' > 'contigs.fasta' &&
91 #else
92 ln -s '$mode.input_fasta' 'contigs.fasta' &&
93 #end if
94 #else 109 #else
95 #if $mode.multi_fasta.select == 'concatenated' 110 #if $mode.multi_fasta.select == 'concatenated'
96 #if $mode.multi_fasta.input_fasta.ext.endswith(".gz") 111 ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
97 gunzip -c '$mode.multi_fasta.input_fasta' > 'contigs.fasta' &&
98 #else
99 ln -s '$mode.multi_fasta.input_fasta' 'contigs.fasta' &&
100 #end if
101 #set $separator = $mode.multi_fasta.separator 112 #set $separator = $mode.multi_fasta.separator
102 #else 113 #else
103 #for $e in $mode.multi_fasta.input_fasta 114 #for $e in $mode.multi_fasta.input_fasta
104 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) 115 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
105 #if $e.ext.endswith(".gz") 116 ln -s '$e' '${identifier}.$e.ext' &&
106 gunzip -c '$e' > '${identifier}.fasta' &&
107 #else
108 ln -s '$e' '${identifier}.fasta' &&
109 #end if
110 #end for 117 #end for
111 #set $separator = ':' 118 #set $separator = ':'
112 SemiBin2 concatenate_fasta 119 SemiBin2 concatenate_fasta
113 --input-fasta *.fasta 120 --input-fasta
121 #for $e in $mode.multi_fasta.input_fasta
122 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
123 '${identifier}.$e.ext'
124 #end for
114 --output 'output' 125 --output 'output'
115 --separator '$separator' 126 --separator '$separator'
116 --compression none 127 --compression none
117 -m $mode.multi_fasta.min_len 128 -m $mode.multi_fasta.min_len
118 && 129 &&
127 <param argument="--input-bam" type="data" format="bam" label="Read mapping to the contigs" help="Sorted BAM files"/> 138 <param argument="--input-bam" type="data" format="bam" label="Read mapping to the contigs" help="Sorted BAM files"/>
128 </xml> 139 </xml>
129 <xml name="input-bam-multi"> 140 <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"/> 141 <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> 142 </xml>
143 <!-- Strobealign files -->
144 <xml name="input-txt">
145 <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/>
146 </xml>
132 <token name="@BAM_FILES@"><![CDATA[ 147 <token name="@BAM_FILES@"><![CDATA[
133 #if $mode.select == 'single' 148 #if $mode.select == 'single'
134 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_bam.element_identifier)) 149 #set $identifier = re.sub('[^\s\w\-]', '_', str($mode.input_bam.element_identifier))
135 ln -s '$input_bam' '${identifier}.bam' && 150 ln -s '$mode.input_bam' '${identifier}.bam' &&
136 #else 151 #else
137 #for $e in $input_bam 152 #for $e in $mode.input_bam
138 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) 153 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
139 ln -s '$e' '${identifier}.bam' && 154 ln -s '$e' '${identifier}.bam' &&
140 #end for 155 #end for
141 #end if 156 #end if
157 ]]></token>
158 <token name="@STROBEALIGN_FILES@"><![CDATA[
159 #for $e in $mode.align_select.abundance
160 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
161 ln -s '$e' '${identifier}.txt' &&
162 #end for
142 ]]></token> 163 ]]></token>
143 <xml name="ref_select_cannot"> 164 <xml name="ref_select_cannot">
144 <param name="select" type="select" label="Reference database"> 165 <param name="select" type="select" label="Reference database">
145 <option value="cached">Cached database</option> 166 <option value="cached">Cached database</option>
146 <option value="taxonomy">Pre-computed taxonomy</option> 167 <option value="taxonomy">Pre-computed taxonomy</option>
255 </xml> 276 </xml>
256 <xml name="orf-finder"> 277 <xml name="orf-finder">
257 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins"> 278 <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> 279 <option value="fast-naive" selected="true">Fast-Naive</option>
259 <option value="prodigal">Prodigal</option> 280 <option value="prodigal">Prodigal</option>
260 <option value="fraggenescan">Fraggenescan</option>
261 </param> 281 </param>
262 </xml> 282 </xml>
263 <xml name="max-node"> 283 <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"/> 284 <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/>
265 </xml> 285 </xml>
291 <xml name="data"> 311 <xml name="data">
292 <param argument="--data" type="data" format="csv" label="Train data"/> 312 <param argument="--data" type="data" format="csv" label="Train data"/>
293 </xml> 313 </xml>
294 <xml name="data_output_single"> 314 <xml name="data_output_single">
295 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data"> 315 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
296 <filter>mode["select"]=="single" or mode["select"]=="co"</filter> 316 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
297 </data> 317 </data>
298 <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data"> 318 <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
299 <filter>mode["select"]=="single" or mode["select"]=="co"</filter> 319 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
300 </data> 320 </data>
301 </xml> 321 </xml>
302 <xml name="data_output_multi"> 322 <xml name="data_output_multi">
303 <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample"> 323 <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
304 <filter>mode["select"]=="multi"</filter> 324 <filter>input_type_select['mode']['select']=="multi"</filter>
305 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> 325 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
306 </collection> 326 </collection>
307 <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample"> 327 <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
308 <filter>mode["select"]=="multi"</filter> 328 <filter>input_type_select['mode']['select']=="multi"</filter>
309 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> 329 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
310 </collection> 330 </collection>
311 </xml> 331 </xml>
312 <xml name="generate_sequence_features_extra_outputs"> 332 <xml name="generate_sequence_features_extra_outputs">
313 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage"> 333 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
314 <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> 334 <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
335 <filter>input_type_select['input_type']=="bam"</filter>
315 </data> 336 </data>
316 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)"> 337 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
317 <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> 338 <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
339 <filter>input_type_select['input_type']=="bam"</filter>
318 </data> 340 </data>
319 <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)"> 341 <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
320 <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> 342 <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
343 <filter>input_type_select['input_type']=="bam"</filter>
321 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" /> 344 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
322 </collection> 345 </collection>
323 <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> 346 <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
324 <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> 347 <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
348 <filter>input_type_select['input_type']=="bam"</filter>
325 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" /> 349 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
326 </collection> 350 </collection>
351 <data name="cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
352 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
353 <filter>input_type_select['input_type']=="txt"</filter>
354 </data>
355 <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
356 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
357 <filter>input_type_select['input_type']=="txt"</filter>
358 </data>
359 <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
360 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
361 <filter>input_type_select['input_type']=="txt"</filter>
362 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
363 </collection>
327 <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)"> 364 <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
328 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> 365 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
366 <filter>input_type_select['input_type']=="bam"</filter>
367 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" recurse="true"/>
368 </collection>
369 <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
370 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
371 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
372 </collection>
373 <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
374 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
375 <filter>input_type_select['input_type']=="bam"</filter>
376 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
377 </collection>
378 <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
379 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
380 <filter>input_type_select['input_type']=="bam"</filter>
381 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" match_relative_path="true" recurse="true"/>
382 </collection>
383 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
384 <filter>input_type_select['mode']['select']=="multi" and extra_output and "contigs" in extra_output</filter>
385 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
386 </collection>
387 </xml>
388 <xml name="generate_sequence_features_extra_outputs_main">
389 <!-- Single -->
390 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
391 <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
392 </data>
393 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
394 <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
395 </data>
396 <!-- Bam co aligned -->
397 <collection name="co_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
398 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
399 <filter>mode['align_select']</filter>
400 <filter>mode['align_select']['align_select']=="bam"</filter>
401 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
402 </collection>
403 <collection name="co_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
404 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
405 <filter>mode['align_select']</filter>
406 <filter>mode['align_select']['align_select']=="bam"</filter>
407 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
408 </collection>
409
410 <!-- Bam Multi aligned -->
411 <collection name="multi_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
412 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
413 <filter>mode['align_select']</filter>
414 <filter>mode['align_select']['align_select']=="bam"</filter>
329 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" /> 415 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
330 </collection> 416 </collection>
331 <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample"> 417 <collection name="multi_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
332 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> 418 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
419 <filter>mode['align_select']</filter>
420 <filter>mode['align_select']['align_select']=="bam"</filter>
333 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> 421 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
334 </collection> 422 </collection>
335 <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)"> 423 <collection name="multi_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
336 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> 424 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
425 <filter>mode['align_select']</filter>
426 <filter>mode['align_select']['align_select']=="bam"</filter>
337 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" /> 427 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
338 </collection> 428 </collection>
339 <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)"> 429 <collection name="multi_split_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
340 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> 430 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
431 <filter>mode['align_select']</filter>
432 <filter>mode['align_select']['align_select']=="bam"</filter>
433 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
434 </collection>
435 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
436 <filter>mode['select']=="multi" and extra_output and "contigs" in extra_output</filter>
437 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
438 </collection>
439 <!-- Txt co aligned -->
440 <data name="co_split_cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
441 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
442 <filter>mode['align_select']</filter>
443 <filter>mode['align_select']['align_select']=="txt"</filter>
444 </data>
445 <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
446 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
447 <filter>mode['align_select']</filter>
448 <filter>mode['align_select']['align_select']=="txt"</filter>
449 </data>
450 <!-- Txt multi aligned -->
451 <collection name="multi_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage per sample (aemb)">
452 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
453 <filter>mode['align_select']</filter>
454 <filter>mode['align_select']['align_select'] =="txt"</filter>
455 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
456 </collection>
457 <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
458 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
459 <filter>mode['align_select']</filter>
460 <filter>mode['align_select']['align_select']=="txt"</filter>
341 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> 461 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
342 </collection> 462 </collection>
343 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
344 <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
345 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
346 </collection>
347
348 </xml> 463 </xml>
349 <xml name="train_output"> 464 <xml name="train_output">
350 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" /> 465 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
351 </xml> 466 </xml>
352 <xml name="cannot_link_output"> 467 <xml name="cannot_link_output">
353 <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" /> 468 <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" />
354 </xml> 469 </xml>
355 <token name="@HELP_HEADER@"><![CDATA[ 470 <token name="@HELP_HEADER@"><![CDATA[
471
356 What it does 472 What it does
357 ============ 473 ============
358 474
359 SemiBin is a Semi-supervised siamese neural network for metagenomic binning 475 SemiBin is a Semi-supervised siamese neural network for metagenomic binning
360 476 ]]></token>
361 ]]></token>
362 <token name="@HELP_INPUT_FASTA@"><![CDATA[ 477 <token name="@HELP_INPUT_FASTA@"><![CDATA[
363 - Contigs in fasta for 1 or several samples from single or co-assembly 478 - Contigs in fasta for 1 or several samples from single or co-assembly
364 ]]></token> 479 ]]></token>
365 <token name="@HELP_INPUT_BAM@"><![CDATA[ 480 <token name="@HELP_INPUT_BAM@"><![CDATA[
366 - BAM with reads mapping to the contigs 481 - BAM with reads mapping to the contigs
367 ]]></token> 482 ]]></token>
483 <token name="@HELP_INPUT_STROBEALIGN@"><![CDATA[
484 - TXT alignment files that are the output of strobealign-aemb
485 ]]></token>
368 <token name="@HELP_CANNOT@"><![CDATA[ 486 <token name="@HELP_CANNOT@"><![CDATA[
369 - Cannot-link constraints 487 - Cannot-link constraints
370 ]]></token> 488 ]]></token>
371 <token name="@HELP_DATA@"><![CDATA[ 489 <token name="@HELP_DATA@"><![CDATA[
372 - Training data and split training data for the model 490 - Training data and split training data for the model
373 ]]></token> 491 ]]></token>
374 <token name="@HELP_MODEL@"><![CDATA[ 492 <token name="@HELP_MODEL@"><![CDATA[
375 - Semi-supervised deep learning model 493 - Semi-supervised deep learning model
376 ]]></token> 494 ]]></token>
377 <token name="@HELP_BINS@"><![CDATA[ 495 <token name="@HELP_BINS@"><![CDATA[
378 - Reconstructed bins after reclustering 496 - Reconstructed bins after reclustering
379 - Reconstructed bins before reclustering 497 - Reconstructed bins before reclustering
380 ]]></token> 498 ]]></token>
381 <xml name="citations"> 499 <xml name="citations">
382 <citations> 500 <citations>
383 <citation type="doi">10.1038/s41467-022-29843-y</citation> 501 <citation type="doi">10.1038/s41467-022-29843-y</citation>
384 </citations> 502 </citations>
385 </xml> 503 </xml>