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comparison macros.xml @ 0:f69397b32f52 draft

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planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b
author estrain
date Fri, 13 Mar 2026 12:21:18 +0000
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-1:000000000000 0:f69397b32f52
1 <macros>
2 <token name="@TOOL_VERSION@">4.2.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
8 </requirements>
9 </xml>
10 <xml name="stdio">
11 <stdio>
12 <exit_code range="1:"/>
13 <regex match="Cannot allocate memory"
14 source="stdout"
15 level="fatal_oom"
16 description="Out of memory error occurred"/>
17 <regex match="The reads contain too many k-mers to fit into available memory"
18 source="stdout"
19 level="fatal_oom"
20 description="Out of memory error occurred"/>
21 </stdio>
22 </xml>
23 <xml name="version_command">
24 <version_command><![CDATA[spades.py --version 2>&1 | awk -F 'v' '{print $2}']]></version_command>
25 </xml>
26 <token name="@FASTA_INTYPES@">fasta,fasta.gz</token>
27 <token name="@FASTQ_INTYPES@">fastqillumina,fastqillumina.gz,fastqsanger,fastqsanger.gz</token>
28 <token name="@INTYPES@">@FASTQ_INTYPES@,@FASTA_INTYPES@</token>
29
30 <xml name="citations">
31 <citations>
32 <citation type="doi">10.1093/bioinformatics/btv688</citation>
33 <citation type="doi">10.1093/bioinformatics/btu266</citation>
34 <citation type="doi">10.1093/bioinformatics/btv337</citation>
35 <yield/>
36 </citations>
37 </xml>
38 <xml name="operation_mode" token_help="">
39 <param name="operation_mode" type="select" label="Operation mode" help="@HELP@">
40 <option value="">Assembly and error correction</option>
41 <option value="--only-assembler">Only assembler (--only-assembler)</option>
42 <option value="--only-error-correction">Only error correction (--only-error-correction)</option>
43 </param>
44 </xml>
45
46 <token name="@OMP_THREADS@"><![CDATA[
47 export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
48 ]]></token>
49
50 <!-- PREPARE INPUT FILES-->
51
52 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
53 #import re
54 #def fix_ext($ext):
55 #set ext = $ext.replace('fastqsanger', 'fastq')
56 #set ext = $ext.replace('fastqillumina', 'fastq')
57 #return $ext
58 #end def
59
60 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"
61 mkdir -p reads1 &&
62 #set file_paths1 = []
63 #for $input_file in $singlePaired.input1
64 #set ext = $fix_ext($input_file.ext)
65 #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
66 #set file_path = 'reads1/' + $fname
67 ln -s '$input_file' '$file_path' &&
68 $file_paths1.append($file_path)
69 #end for
70 #else
71 ## one mapped-in paired dataset (Galaxy maps list:paired -> 1 job per pair)
72 mkdir -p paired_reads1 &&
73 #set fw_reads1 = []
74 #set rv_reads1 = []
75 #set ext = $fix_ext($singlePaired.input.forward.ext)
76 #set base = re.sub('[^\w\-_.]', '_', $singlePaired.input.element_identifier)
77 #set f1 = 'paired_reads1/' + $base + '1.' + $ext
78 #set f2 = 'paired_reads1/' + $base + '2.' + $ext
79 ln -s '$singlePaired.input.forward' '$f1' &&
80 ln -s '$singlePaired.input.reverse' '$f2' &&
81 $fw_reads1.append($f1)
82 $rv_reads1.append($f2)
83 #end if
84 ]]></token>
85
86 <token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[
87 #if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced"
88 mkdir -p reads2 &&
89 #set file_paths2 = []
90 #for $input_file in $additional_reads.singlePaired.input1
91 #set ext = $fix_ext($input_file.ext)
92 #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
93 #set file_path = 'reads2/' + $fname
94 ln -s '$input_file' '$file_path' &&
95 $file_paths2.append($file_path)
96 #end for
97 #else
98 ## one mapped-in paired dataset for the additional library
99 mkdir -p paired_reads2 &&
100 #set fw_reads2 = []
101 #set rv_reads2 = []
102 #set ext = $fix_ext($additional_reads.singlePaired.input.forward.ext)
103 #set base = re.sub('[^\w\-_.]', '_', $additional_reads.singlePaired.input.element_identifier)
104 #set f1 = 'paired_reads2/' + $base + '1.' + $ext
105 #set f2 = 'paired_reads2/' + $base + '2.' + $ext
106 ln -s '$additional_reads.singlePaired.input.forward' '$f1' &&
107 ln -s '$additional_reads.singlePaired.input.reverse' '$f2' &&
108 $fw_reads2.append($f1)
109 $rv_reads2.append($f2)
110 #end if
111 ]]></token>
112
113 <!-- COMMANDS -->
114
115 <token name="@RESOURCES@"><![CDATA[
116 -t \${GALAXY_SLOTS:-4}
117 -m \$((\${GALAXY_MEMORY_MB:-8192}/1024))
118 --tmp-dir \${TMPDIR}
119 ]]></token>
120
121 <token name="@INPUT_READS_MAIN@"><![CDATA[
122 #if $singlePaired.sPaired == "single"
123 #for $read in $file_paths1
124 --s $library '${read}'
125 #end for
126 #else if $singlePaired.sPaired == "paired_interlaced"
127 #for $read in $file_paths1
128 --${singlePaired.type_paired}-12 $library '${read}'
129 --${singlePaired.type_paired}-or $library $singlePaired.orientation
130 #end for
131 #else
132 #for $read in $fw_reads1
133 --${singlePaired.type_paired}-1 $library '${read}'
134 #end for
135 #for $read in $rv_reads1
136 --${singlePaired.type_paired}-2 $library '${read}'
137 --${singlePaired.type_paired}-or $library $singlePaired.orientation
138 #end for
139 #end if
140 ]]></token>
141
142
143 <token name="@INPUT_READS_ADDITIONAL@"><![CDATA[
144 @LIBRARY_NUMBER@
145 #if $additional_reads.singlePaired.sPaired == "single"
146 #for $read in $file_paths2
147 --s $library '${read}'
148 #end for
149 #else if $additional_reads.singlePaired.sPaired == "paired_interlaced"
150 #for $read in $file_paths2
151 --${additional_reads.singlePaired.type_paired}-12 $library '${read}'
152 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
153 #end for
154 #else
155 #for $read in $fw_reads2
156 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
157 #end for
158 #for $read in $rv_reads2
159 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
160 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
161 #end for
162 #end if
163 ]]></token>
164
165 <token name="@PIPELINE_OPTIONS@"><![CDATA[
166 #for $i in $mode_sel
167 $i
168 #end for
169 ]]></token>
170
171 <token name="@KMER@"><![CDATA[
172 #if $kmer_cond.kmer_sel != 'auto'
173 -k '$kmer_cond.manual'
174 #end if
175 ]]></token>
176
177 <token name="@PHREDOFFSET@"><![CDATA[
178 #if $phred_offset != 'auto'
179 --phred-offset $phred_offset
180 #end if
181 ]]></token>
182
183 <!-- ADDITIONAL INPUTS-->
184
185 <token name="@PREPROCESS_CONTIGS_FILES@"><![CDATA[
186 #if $arf.trusted_contigs
187 mkdir -p trusted_contigs &&
188 #set trusted_contigs = []
189 #for $i, $input_file in enumerate($arf.trusted_contigs,1)
190 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
191 #set $fname = 'file' + str($i) + '.' + $ext
192 #set $file_path = 'trusted_contigs/' + $fname
193 ln -s '$input_file' '$file_path' &&
194 $trusted_contigs.append($file_path)
195 #end for
196 #end if
197 #if $arf.untrusted_contigs
198 mkdir -p untrusted_contigs &&
199 #set untrusted_contigs = []
200 #for $i, $input_file in enumerate($arf.untrusted_contigs,1)
201 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
202 #set $fname = 'file' + str($i) + '.' + $ext
203 #set $file_path = 'untrusted_contigs/' + $fname
204 ln -s '$input_file' '$file_path' &&
205 $untrusted_contigs.append($file_path)
206 #end for
207 #end if
208 ]]></token>
209
210 <token name="@PREPROCESS_NANOPORE_PACBIO_FILES@"><![CDATA[
211 #if $arf.nanopore
212 mkdir -p nanopore_reads &&
213 #set nanopore_reads = []
214 #for $i, $input_file in enumerate($arf.nanopore,1)
215 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
216 #set $fname = 'file' + str($i) + '.' + $ext
217 #set $file_path = 'nanopore_reads/' + $fname
218 ln -s '$input_file' '$file_path' &&
219 $nanopore_reads.append($file_path)
220 #end for
221 #end if
222 #if $arf.pacbio
223 mkdir -p pacbio_reads &&
224 #set pacbio_reads = []
225 #for $i, $input_file in enumerate($arf.pacbio,1)
226 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
227 #set $fname = 'file' + str($i) + '.' + $ext
228 #set $file_path = 'pacbio_reads/' + $fname
229 ln -s '$input_file' '$file_path' &&
230 $pacbio_reads.append($file_path)
231 #end for
232 #end if
233 ]]></token>
234
235 <token name="@PREPROCESS_SANGER_FILES@"><![CDATA[
236 #if $arf.sanger
237 mkdir -p sanger_reads &&
238 #set sanger_reads = []
239 #for $i, $input_file in enumerate($arf.sanger,1)
240 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
241 #set $fname = 'file' + str($i) + '.' + $ext
242 #set $file_path = 'sanger_reads/' + $fname
243 ln -s '$input_file' '$file_path' &&
244 $sanger_reads.append($file_path)
245 #end for
246 #end if
247 ]]></token>
248
249 <token name="@PREPROCESS_FL_RNA_FILES@"><![CDATA[
250 #if $arf.flrna
251 mkdir -p flrna_reads &&
252 #set flrna_reads = []
253 #for $i, $input_file in enumerate($arf.flrna,1)
254 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
255 #set $fname = 'file' + str($i) + '.' + $ext
256 #set $file_path = 'flrna_reads/' + $fname
257 ln -s '$input_file' '$file_path' &&
258 $flrna_reads.append($file_path)
259 #end for
260 #end if
261 ]]></token>
262
263 <token name="@PREPROCESS_ASSEMBLY_GRAPH_FILES@"><![CDATA[
264 #if $arf.assembly_graph
265 mkdir -p assembly_graphs &&
266 #set assembly_graphs = []
267 #for $i, $input_file in enumerate($arf.assembly_graph,1)
268 #set $ext = $input_file.ext.replace('gfa1', 'gfa')
269 #set $fname = 'file' + str($i) + '.' + $ext
270 #set $file_path = 'assembly_graphs/' + $fname
271 ln -s '$input_file' '$file_path' &&
272 $assembly_graphs.append($file_path)
273 #end for
274 #end if
275 ]]></token>
276
277
278 <token name="@NANOPORE_PACBIO@"><![CDATA[
279 #if $arf.nanopore
280 #for $read in $nanopore_reads
281 --nanopore $read
282 #end for
283 #end if
284 #if $arf.pacbio
285 #for $read in $pacbio_reads
286 --pacbio $read
287 #end for
288 #end if
289 ]]></token>
290
291
292 <token name="@SANGER@"><![CDATA[
293 #if $arf.sanger
294 #for $read in $sanger_reads
295 --sanger $read
296 #end for
297 #end if
298 ]]></token>
299
300 <token name="@FL_RNA@"><![CDATA[
301 #if $arf.flrna
302 #for $read in $flrna_reads
303 --fl-rna $read
304 #end for
305 #end if
306 ]]></token>
307
308 <token name="@ASSEMBLY_GRAPH@"><![CDATA[
309 #if $arf.assembly_graph
310 #for $graph in $assembly_graphs
311 --assembly-graph $graph
312 #end for
313 #end if
314 ]]></token>
315
316 <token name="@CONTIGS@"><![CDATA[
317 #if $arf.trusted_contigs
318 #for $read in $trusted_contigs
319 --trusted-contigs $read
320 #end for
321 #end if
322 #if $arf.untrusted_contigs
323 #for $read in $untrusted_contigs
324 --untrusted-contigs $read
325 #end for
326 #end if
327 ]]></token>
328
329 <token name="@LIBRARY_NUMBER@"><![CDATA[
330 #if $additional_reads.selector == 'true' and $additional_reads.library_number == 'false'
331 #set $library += 1
332 #end if
333 ]]></token>
334
335 <!-- POSTPROCESSING -->
336
337 <token name="@STATS@"><![CDATA[
338 #if 'cs' in $optional_output
339 && (test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.')
340 #end if
341 #if 'ss' in $optional_output
342 && (test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.')
343 #end if
344 ]]></token>
345
346 <!--
347 input
348 -->
349
350 <xml name="input_files_all" token_format="" token_label="" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
351 <conditional name="singlePaired">
352 <param name="sPaired" type="select" label="Single-end or paired-end short-reads" help="@HELP@">
353 <option value="single">Single-end</option>
354 <option value="paired_interlaced">Paired-end: interlaced reads</option>
355 <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option>
356 </param>
357 <when value="single">
358 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@"/>
359 </when>
360 <when value="paired_interlaced">
361 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
362 <expand macro="type_paired"/>
363 <expand macro="orientation"/>
364 </when>
365 <when value="paired_collection">
366 <!-- CHANGED: list:paired -> paired (Galaxy maps lists) -->
367 <param format="@FORMAT@" name="input" type="data_collection" collection_type="paired" label="@LABEL@: collection (a single pair; lists will map)"/>
368 <expand macro="type_paired"/>
369 <expand macro="orientation"/>
370 </when>
371 </conditional>
372 </xml>
373
374 <xml name="input_files_paired" tokens="format,label" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
375 <conditional name="singlePaired">
376 <param name="sPaired" type="select" label="Pair-end reads input format" help="@HELP@">
377 <option value="paired_interlaced">Paired-end: interlaced reads</option>
378 <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option>
379 </param>
380 <when value="paired_interlaced">
381 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
382 <expand macro="type_paired"/>
383 <expand macro="orientation"/>
384 </when>
385 <when value="paired_collection">
386 <!-- CHANGED: list:paired -> paired -->
387 <param format="@FORMAT@" name="input" type="data_collection" collection_type="paired" label="@LABEL@: collection (a single pair; lists will map)"/>
388 <expand macro="type_paired"/>
389 <expand macro="orientation"/>
390 </when>
391 </conditional>
392 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the same sample, it means that they belong to the same library.">
393 <option value="true" selected="true">True</option>
394 <option value="false">False</option>
395 </param>
396 </xml>
397
398 <xml name="orientation">
399 <param name="orientation" type="select" label="Select orientation of reads" help="Note: mate-pair fragments are generally in a RF conformation. In general, paired-end reads tend to be in a FR orientation.">
400 <option value="fr" selected="true"><![CDATA[FR (-> <-)]]></option>
401 <option value="rf"><![CDATA[RF (<- ->)]]></option>
402 <option value="ff"><![CDATA[FF (-> ->)]]></option>
403 </param>
404 </xml>
405
406 <xml name="type_paired">
407 <param name="type_paired" type="select" label="Type of paired-reads"
408 help="In paired-end sequencing, the library preparation yields a set of fragments, and the machine sequences each fragment from both ends. In mate-pair sequencing,
409 the library preparation yields two fragments that are distal to each other in the genome and in the opposite in orientation to that of a mate-paired fragment.">
410 <option value="pe" selected="true">Default (--pe)</option>
411 <option value="mp">Mate-pair reads (--mp)</option>
412 <option value="hqmp">High-quality Nextera mate-pair reads (--hqmp)</option>
413 </param>
414 </xml>
415
416 <xml name="input_additional_files_all" tokens="format" token_help="">
417 <conditional name="additional_reads">
418 <param name="selector" type="select" label="Use an additional set of short-reads" help="Enable this option if you want to combine to data sources (e.g. single and paired reads).">
419 <option value="false" selected="true">Disabled</option>
420 <option value="true">Enabled</option>
421 </param>
422 <when value="true">
423 <expand macro="input_files_all" format="@FORMAT@" label="FASTA/FASTQ file(s)" help="@HELP@"/>
424 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
425 <option value="true" selected="true">True</option>
426 <option value="false">False</option>
427 </param>
428 </when>
429 <when value="false"/>
430 </conditional>
431 </xml>
432
433 <xml name="input_additional_files_paired" tokens="format" token_help="" >
434 <conditional name="additional_reads">
435 <param name="selector" type="select" label="Use an additional set of short-reads" help="Enable this option if you want to combine to data sources (e.g. single and paired reads).">
436 <option value="false" selected="true">Disabled</option>
437 <option value="true">Enabled</option>
438 </param>
439 <when value="true">
440 <expand macro="input_files_paired" format="@FORMAT@" label="FASTA/FASTQ file(s)" help="@HELP@"/>
441 </when>
442 <when value="false"/>
443 </conditional>
444 </xml>
445
446 <xml name="covcutoff">
447 <conditional name="cov_cond">
448 <param argument="--cov-cutoff" type="select" label="Set coverage cutoff option" help="When set to 'auto' SPAdes automatically computes coverage threshold using conservative strategy">
449 <option value="off">Off</option>
450 <option value="auto">Auto</option>
451 <option value="value">User specific</option>
452 </param>
453 <when value="off"/>
454 <when value="auto"/>
455 <when value="value">
456 <param name="manual" type="float" min="0" value="" label="Set value"/>
457 </when>
458 </conditional>
459 </xml>
460 <xml name="pipeline_options" token_additional_help="">
461 <param name="mode_sel" type="select" label="Pipeline options" multiple="true" optional="true" display="checkboxes" help="Error correction requires FASTQ input files. @ADDITIONAL_HELP@">
462 <option value="--disable-rr">Disable repeat resolution (--disable-rr)</option>
463 <yield/>
464 </param>
465 </xml>
466 <xml name="kmer" token_help="" token_default="21,33,55,77">
467 <conditional name="kmer_cond">
468 <param name="kmer_sel" argument="-k" type="select" label="Select k-mer detection option" help="@HELP@ Comma-separated list, all values must be odd, less than 128 and listed in ascending order.">
469 <option value="auto">Auto</option>
470 <option value="manual">User specific</option>
471 </param>
472 <when value="auto"/>
473 <when value="manual">
474 <param name="manual" type="text" value="@DEFAULT@" label="K-mer size values" help="List of k-mer sizes (must be odd and less than 128)">
475 <sanitizer invalid_char="">
476 <valid initial="string.digits">
477 <add value="," />
478 </valid>
479 </sanitizer>
480 <validator type="regex">[0-9,]+</validator>
481 </param>
482 </when>
483 </conditional>
484 </xml>
485 <xml name="nanopore_pacbio">
486 <param argument="--nanopore" type="data" format="@FASTQ_INTYPES@" multiple="true" optional="true" label="Nanopore reads" help="SPAdes will use Oxford Nanopore reads for gap closure and repeat resolution"/>
487 <param argument="--pacbio" type="data" format="@FASTQ_INTYPES@" multiple="true" optional="true" label="PacBio CLR reads" help="It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5). In addition, SPAdes develpers suggest not to run SPAdes on PacBio reads for large genomes. SPAdes will use PacBio CLR reads for gap closure and repeat resolution"/>
488 </xml>
489 <xml name="flrna">
490 <param argument="--fl-rna" name="flrna" type="data" format="@INTYPES@" multiple="true" optional="true" label="PacBio/Nanopore/contigs that capture full-length transcripts" help="In addition to long reads, you may also provide a separate file with reads capturing the entire transcript sequences using this option. Full-length transcripts in such reads can be typically detected using the adapters. Note, that FL reads should be trimmed so that the adapters are excluded."/>
491 </xml>
492
493 <xml name="phred">
494 <param argument="--phred-offset" type="select" label="Set Phred quality offset" help="Phred quality offset in the input reads. Default: auto-detect">
495 <option value="auto" selected="true">Auto</option>
496 <option value="33">33 (Sanger)</option>
497 <option value="64">64 (Illumina)</option>
498 </param>
499 </xml>
500 <xml name="reads" token_paramname="reads" token_help="" token_label="">
501 <param name="@PARAMNAME@" type="data" format="@FASTQ_INTYPES@" label="@LABEL@ reads" help="@HELP@"/>
502 </xml>
503 <xml name="sanger">
504 <param argument="--sanger" type="data" format="@FASTQ_INTYPES@" multiple="true" optional="true" label="Sanger reads"/>
505 </xml>
506 <xml name="contigs">
507 <param argument="--trusted-contigs" type="data" format="@FASTA_INTYPES@" multiple="true" optional="true" label="Trusted contigs" help="Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species."/>
508 <param argument="--untrusted-contigs" type="data" format="@FASTA_INTYPES@" multiple="true" optional="true" label="Untrusted contigs" help="Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species."/>
509 </xml>
510 <xml name="assembly_graph">
511 <param argument="--assembly-graph" type="data" format="gfa1" multiple="true" optional="true" label="Assembly graphs" help=" The primary purpose of this option to run these pipelines on already constructed and simplified assembly graph this way skipping a large part of SPAdes pipeline."/>
512 </xml>
513 <xml name="optional_output">
514 <param name="optional_output" type="select" multiple="true" optional="false" label="Select optional output file(s)" help="Only shown in history if selected here and generated by the specific run.">
515 <option value="ag" selected="true">Assembly graph</option>
516 <option value="ags" selected="true">Assembly graph with scaffolds</option>
517 <option value="cn" selected="true">Contigs</option>
518 <option value="cp">Contigs paths</option>
519 <option value="cr">Corrected reads</option>
520 <option value="cs">Contigs stats</option>
521 <option value="l">Log</option>
522 <option value="sc" selected="true">Scaffolds</option>
523 <option value="sp">Scaffolds paths</option>
524 <option value="ss">Scaffolds stats</option>
525 </param>
526 </xml>
527 <!--
528 output macros (unchanged; Galaxy will collect into a list when mapped)
529 -->
530
531 <xml name="out_ag">
532 <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph">
533 <filter>'ag' in optional_output</filter>
534 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
535 </data>
536 </xml>
537 <xml name="out_ags">
538 <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds">
539 <filter>'ags' in optional_output</filter>
540 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
541 </data>
542 </xml>
543 <xml name="out_cn">
544 <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs">
545 <filter>'cn' in optional_output</filter>
546 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
547 </data>
548 </xml>
549 <xml name="out_cp">
550 <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths">
551 <filter>'cp' in optional_output</filter>
552 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
553 </data>
554 </xml>
555 <xml name="out_cr">
556 <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads">
557 <filter>'cr' in optional_output</filter>
558 <filter>'operation_mode' not in vars() or operation_mode != '--only-assembler'</filter>
559 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.cor\.fastq\.gz" format="fastq" directory="output/corrected"/>
560 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.cor\.fasta\.gz" format="fasta" directory="output/corrected"/>
561 </collection>
562 </xml>
563 <xml name="out_cs">
564 <data name="out_cs" format="tabular" label="${tool.name} on ${on_string}: Contigs stats">
565 <actions>
566 <action name="column_names" type="metadata" default="name,length,coverage"/>
567 </actions>
568 <filter>'cs' in optional_output</filter>
569 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
570 </data>
571 </xml>
572 <xml name="out_l">
573 <data name="out_l" format="txt" from_work_dir="output/spades.log" label="${tool.name} on ${on_string}: Log">
574 <filter>'l' in optional_output</filter>
575 </data>
576 </xml>
577 <xml name="out_sc">
578 <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds">
579 <filter>'sc' in optional_output</filter>
580 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
581 </data>
582 </xml>
583 <xml name="out_sp">
584 <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths">
585 <filter>'sp' in optional_output</filter>
586 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
587 </data>
588 </xml>
589 <xml name="out_ss">
590 <data name="out_ss" format="tabular" label="${tool.name} on ${on_string}: Scaffolds stats">
591 <actions>
592 <action name="column_names" type="metadata" default="name,length,coverage"/>
593 </actions>
594 <filter>'ss' in optional_output</filter>
595 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
596 </data>
597 </xml>
598 <xml name="out_rs">
599 <data name="out_rs" format="fasta" from_work_dir="output/raw_scaffolds.fasta" label="${tool.name} on ${on_string}: Raw scaffolds">
600 <filter>'rs' in optional_output</filter>
601 </data>
602 </xml>
603 <xml name="out_b">
604 <data name="out_b" format="txt" from_work_dir="output/hmm_statistics.txt" label="${tool.name} on ${on_string}: HMM statistics">
605 <filter>'b' in optional_output</filter>
606 </data>
607 </xml>
608 <xml name="out_dg">
609 <data name="out_dg" format="fasta" from_work_dir="output/domain_graph.dot" label="${tool.name} on ${on_string}: Domain graph">
610 <filter>'dg' in optional_output</filter>
611 </data>
612 </xml>
613
614 <!-- help tokens unchanged -->
615 <token name="@HELP_IN@"><![CDATA[
616 ... (unchanged help text) ...
617 ]]></token>
618 <token name="@HELP_OUT_AG@">- Assembly graph</token>
619 <token name="@HELP_OUT_AGS@">- Assembly graph with scaffolds</token>
620 <token name="@HELP_OUT_C@">- Contigs</token>
621 <token name="@HELP_OUT_CP@">- Contigs paths in the assembly graph</token>
622 <token name="@HELP_OUT_CS@">- Contigs stats</token>
623 <token name="@HELP_OUT_CR@">- Corrected reads by BayesHammer</token>
624 <token name="@HELP_OUT_L@">- Log file</token>
625 <token name="@HELP_OUT_S@">- Scaffolds (recommended for use as resulting sequences)</token>
626 <token name="@HELP_OUT_SP@">- Scaffolds paths in the assembly graph</token>
627 <token name="@HELP_OUT_SS@">- Scaffolds stats</token>
628 <token name="@HELP_WID@">SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.</token>
629 <token name="@IONTORRENT@"><![CDATA[
630 ... (unchanged IonTorrent help) ...
631 ]]></token>
632
633 </macros>
634