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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
author iuc
date Wed, 12 Mar 2025 21:47:35 +0000
parents ea83ac535a1f
children
comparison
equal deleted inserted replaced
10:ea83ac535a1f 11:6766a94ef559
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.15.5</token> 2 <token name="@TOOL_VERSION@">4.1.0</token>
3 <token name="@VERSION_SUFFIX@">3</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
7 <requirement type="package" version="3.0">zip</requirement>
8 <yield/> 7 <yield/>
9 </requirements> 8 </requirements>
10 </xml> 9 </xml>
11 <xml name="stdio"> 10 <xml name="stdio">
12 <stdio> 11 <stdio>
22 </stdio> 21 </stdio>
23 </xml> 22 </xml>
24 <xml name="version_command"> 23 <xml name="version_command">
25 <version_command><![CDATA[spades.py --version 2>&1 | awk -F 'v' '{print $2}']]></version_command> 24 <version_command><![CDATA[spades.py --version 2>&1 | awk -F 'v' '{print $2}']]></version_command>
26 </xml> 25 </xml>
27 <token name="@INTYPES@"> 26 <token name="@FASTA_INTYPES@">fasta,fasta.gz</token>
28 27 <token name="@FASTQ_INTYPES@">fastqillumina,fastqillumina.gz,fastqsanger,fastqsanger.gz</token>
29 </token> 28 <token name="@INTYPES@">@FASTQ_INTYPES@,@FASTA_INTYPES@</token>
29
30 <xml name="citations"> 30 <xml name="citations">
31 <citations> 31 <citations>
32 <citation type="doi">10.1093/bioinformatics/btv688</citation> 32 <citation type="doi">10.1093/bioinformatics/btv688</citation>
33 <citation type="doi">10.1093/bioinformatics/btu266</citation> 33 <citation type="doi">10.1093/bioinformatics/btu266</citation>
34 <citation type="doi">10.1093/bioinformatics/btv337</citation> 34 <citation type="doi">10.1093/bioinformatics/btv337</citation>
48 ]]></token> 48 ]]></token>
49 49
50 <!-- PREPARE INPUT FILES--> 50 <!-- PREPARE INPUT FILES-->
51 51
52 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[ 52 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
53 #import re
54 #def fix_ext($ext):
55 #set ext = $ext.replace('fastqsanger', 'fastq')
56 #set ext = $ext.replace('fastqillumina', 'fastq')
57 #return $ext
58 #end def
59
53 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced" 60 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"
54 mkdir -p reads1 && 61 mkdir -p reads1 &&
55 #set file_paths1 = [] 62 #set file_paths1 = []
56 #for $input_file in $singlePaired.input1 63 #for $input_file in $singlePaired.input1
57 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 64 #set ext = $fix_ext($input_file.ext)
58 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext 65 #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
59 #set $file_path = 'reads1/' + $fname 66 #set file_path = 'reads1/' + $fname
60 ln -s '$input_file' '$file_path' && 67 ln -s '$input_file' '$file_path' &&
61 $file_paths1.append($file_path) 68 $file_paths1.append($file_path)
62 #end for 69 #end for
63 #else if $singlePaired.sPaired == "paired"
64 mkdir -p paired_reads1 &&
65 #set fw_reads1 = []
66 #for $input_file in $singlePaired.input1
67 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
68 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
69 #set $file_path = 'paired_reads1/' + str($fname)
70 ln -s '$input_file' '$file_path' &&
71 $fw_reads1.append($file_path)
72 #end for
73 #set rv_reads1 = []
74 #for $input_file in $singlePaired.input2
75 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
76 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
77 #set $file_path = 'paired_reads1/' + str($fname)
78 ln -s '$input_file' '$file_path' &&
79 $rv_reads1.append($file_path)
80 #end for
81 #silent $fw_reads1.sort()
82 #silent $rv_reads1.sort()
83 #else 70 #else
84 mkdir -p paired_reads1 && 71 mkdir -p paired_reads1 &&
85 #set fw_reads1 = [] 72 #set fw_reads1 = []
86 #set rv_reads1 = [] 73 #set rv_reads1 = []
87 #for $i, $input_file in enumerate($singlePaired.input) 74 #for $i, $input_file in enumerate($singlePaired.input)
88 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq') 75 #set ext = $fix_ext($input_file.forward.ext)
89 #set $file_path = 'paired_reads1/fw' + str($i) + '.' + $ext 76 #set file_path = 'paired_reads1/' + re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '1.' + $ext
90 ln -s '$input_file.forward' '$file_path' && 77 ln -s '$input_file.forward' '$file_path' &&
91 $fw_reads1.append($file_path) 78 $fw_reads1.append($file_path)
92 #set $file_path = 'paired_reads1/rv' + str($i) + '.' + $ext 79 #set file_path = 'paired_reads1/' + re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '2.' + $ext
93 ln -s '$input_file.reverse' '$file_path' && 80 ln -s '$input_file.reverse' '$file_path' &&
94 $rv_reads1.append($file_path) 81 $rv_reads1.append($file_path)
95 #end for 82 #end for
96 #end if 83 #end if
97 ]]></token> 84 ]]></token>
99 <token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[ 86 <token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[
100 #if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced" 87 #if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced"
101 mkdir -p reads2 && 88 mkdir -p reads2 &&
102 #set file_paths2 = [] 89 #set file_paths2 = []
103 #for $input_file in $additional_reads.singlePaired.input1 90 #for $input_file in $additional_reads.singlePaired.input1
104 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 91 #set ext = $fix_ext($input_file.ext)
105 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext 92 #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
106 #set $file_path = 'reads2/' + $fname 93 #set file_path = 'reads2/' + $fname
107 ln -s '$input_file' '$file_path' && 94 ln -s '$input_file' '$file_path' &&
108 $file_paths2.append($file_path) 95 $file_paths2.append($file_path)
109 #end for 96 #end for
110 #else if $additional_reads.singlePaired.sPaired == "paired"
111 mkdir -p paired_reads2 &&
112 #set fw_reads2 = []
113 #for $input_file in $additional_reads.singlePaired.input1
114 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
115 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
116 #set $file_path = 'paired_reads2/' + str($fname)
117 ln -s '$input_file' '$file_path' &&
118 $fw_reads2.append($file_path)
119 #end for
120 #set rv_reads2 = []
121 #for $input_file in $additional_reads.singlePaired.input2
122 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
123 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
124 #set $file_path = 'paired_reads2/' + str($fname)
125 ln -s '$input_file' '$file_path' &&
126 $rv_reads2.append($file_path)
127 #end for
128 #silent $fw_reads2.sort()
129 #silent $rv_reads2.sort()
130 #else 97 #else
131 mkdir -p paired_reads2 && 98 mkdir -p paired_reads2 &&
132 #set fw_reads2 = [] 99 #set fw_reads2 = []
133 #set rv_reads2 = [] 100 #set rv_reads2 = []
134 #for $i, $input_file in enumerate($additional_reads.singlePaired.input) 101 #for $i, $input_file in enumerate($additional_reads.singlePaired.input)
135 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq') 102 #set ext = $fix_ext($input_file.forward.ext)
136 #set $file_path = 'paired_reads2/fw' + str($i) + '.' + $ext 103 #set file_path = 'paired_reads2/' + re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '1.' + $ext
137 ln -s '$input_file.forward' '$file_path' && 104 ln -s '$input_file.forward' '$file_path' &&
138 $fw_reads2.append($file_path) 105 $fw_reads2.append($file_path)
139 #set $file_path = 'paired_reads2/rv' + str($i) + '.' + $ext 106 #set file_path = 'paired_reads2/' + re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '2.' + $ext
140 ln -s '$input_file.reverse' '$file_path' && 107 ln -s '$input_file.reverse' '$file_path' &&
141 $rv_reads2.append($file_path) 108 $rv_reads2.append($file_path)
142 #end for 109 #end for
143 #end if 110 #end if
144 ]]></token> 111 ]]></token>
153 120
154 <token name="@INPUT_READS_MAIN@"><![CDATA[ 121 <token name="@INPUT_READS_MAIN@"><![CDATA[
155 #if $singlePaired.sPaired == "single" 122 #if $singlePaired.sPaired == "single"
156 #for $read in $file_paths1 123 #for $read in $file_paths1
157 --s $library '${read}' 124 --s $library '${read}'
158 #end for
159 #else if $singlePaired.sPaired == "paired"
160 #for $read in $fw_reads1
161 --${singlePaired.type_paired}-1 $library '${read}'
162 #end for
163 #for $read in $rv_reads1
164 --${singlePaired.type_paired}-2 $library '${read}'
165 --${singlePaired.type_paired}-or $library $singlePaired.orientation
166 #end for 125 #end for
167 #else if $singlePaired.sPaired == "paired_interlaced" 126 #else if $singlePaired.sPaired == "paired_interlaced"
168 #for $read in $file_paths1 127 #for $read in $file_paths1
169 --${singlePaired.type_paired}-12 $library '${read}' 128 --${singlePaired.type_paired}-12 $library '${read}'
170 --${singlePaired.type_paired}-or $library $singlePaired.orientation 129 --${singlePaired.type_paired}-or $library $singlePaired.orientation
184 <token name="@INPUT_READS_ADDITIONAL@"><![CDATA[ 143 <token name="@INPUT_READS_ADDITIONAL@"><![CDATA[
185 @LIBRARY_NUMBER@ 144 @LIBRARY_NUMBER@
186 #if $additional_reads.singlePaired.sPaired == "single" 145 #if $additional_reads.singlePaired.sPaired == "single"
187 #for $read in $file_paths2 146 #for $read in $file_paths2
188 --s $library '${read}' 147 --s $library '${read}'
189 #end for
190 #else if $additional_reads.singlePaired.sPaired == "paired"
191 #for $read in $fw_reads2
192 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
193 #end for
194 #for $read in $rv_reads2
195 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
196 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
197 #end for 148 #end for
198 #else if $additional_reads.singlePaired.sPaired == "paired_interlaced" 149 #else if $additional_reads.singlePaired.sPaired == "paired_interlaced"
199 #for $read in $file_paths2 150 #for $read in $file_paths2
200 --${additional_reads.singlePaired.type_paired}-12 $library '${read}' 151 --${additional_reads.singlePaired.type_paired}-12 $library '${read}'
201 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation 152 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
390 #if 'ss' in $optional_output 341 #if 'ss' in $optional_output
391 && (test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.') 342 && (test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.')
392 #end if 343 #end if
393 ]]></token> 344 ]]></token>
394 345
395 <token name="@CORRECTED@"><![CDATA[
396 #if 'corrected' in $optional_output
397 && (test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.')
398 #end if
399 ]]></token>
400
401 <!-- 346 <!--
402 input 347 input
403 --> 348 -->
404 349
405 <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."> 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.">
406 <conditional name="singlePaired"> 351 <conditional name="singlePaired">
407 <param name="sPaired" type="select" label="Single-end or paired-end short-reads" help="@HELP@"> 352 <param name="sPaired" type="select" label="Single-end or paired-end short-reads" help="@HELP@">
408 <option value="single" selected="true">Single-end</option> 353 <option value="single">Single-end</option>
409 <option value="paired">Paired-end: individual datasets</option>
410 <option value="paired_interlaced">Paired-end: interlaced reads</option> 354 <option value="paired_interlaced">Paired-end: interlaced reads</option>
411 <option value="paired_collection">Paired-end: list of dataset pairs</option> 355 <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option>
412 </param> 356 </param>
413 <when value="single"> 357 <when value="single">
414 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@"/> 358 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@"/>
415 </when>
416 <when value="paired">
417 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: forward reads"/>
418 <param format="@FORMAT@" name="input2" type="data" multiple="true" label="@LABEL@: reverse reads"/>
419 <expand macro="type_paired"/>
420 <expand macro="orientation"/>
421 </when> 359 </when>
422 <when value="paired_interlaced"> 360 <when value="paired_interlaced">
423 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/> 361 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
424 <expand macro="type_paired"/> 362 <expand macro="type_paired"/>
425 <expand macro="orientation"/> 363 <expand macro="orientation"/>
430 <expand macro="orientation"/> 368 <expand macro="orientation"/>
431 </when> 369 </when>
432 </conditional> 370 </conditional>
433 </xml> 371 </xml>
434 372
435 <xml name="input_files_paired" 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."> 373 <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.">
436 <conditional name="singlePaired"> 374 <conditional name="singlePaired">
437 <param name="sPaired" type="select" label="Pair-end reads input format" help="@HELP@"> 375 <param name="sPaired" type="select" label="Pair-end reads input format" help="@HELP@">
438 <option value="paired" selected="true">Paired-end: individual datasets</option>
439 <option value="paired_interlaced">Paired-end: interlaced reads</option> 376 <option value="paired_interlaced">Paired-end: interlaced reads</option>
440 <option value="paired_collection">Paired-end: list of dataset pairs</option> 377 <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option>
441 </param> 378 </param>
442 <when value="paired">
443 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: forward reads"/>
444 <param format="@FORMAT@" name="input2" type="data" multiple="true" label="@LABEL@: reverse reads"/>
445 <expand macro="type_paired"/>
446 <expand macro="orientation"/>
447 </when>
448 <when value="paired_interlaced"> 379 <when value="paired_interlaced">
449 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/> 380 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
450 <expand macro="type_paired"/> 381 <expand macro="type_paired"/>
451 <expand macro="orientation"/> 382 <expand macro="orientation"/>
452 </when> 383 </when>
478 <option value="mp">Mate-pair reads (--mp)</option> 409 <option value="mp">Mate-pair reads (--mp)</option>
479 <option value="hqmp">High-quality Nextera mate-pair reads (--hqmp)</option> 410 <option value="hqmp">High-quality Nextera mate-pair reads (--hqmp)</option>
480 </param> 411 </param>
481 </xml> 412 </xml>
482 413
483 <xml name="input_additional_files_all" token_format="" token_label="" token_help=""> 414 <xml name="input_additional_files_all" tokens="format" token_help="">
484 <conditional name="additional_reads"> 415 <conditional name="additional_reads">
485 <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)."> 416 <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).">
486 <option value="false" selected="true">Disabled</option> 417 <option value="false" selected="true">Disabled</option>
487 <option value="true">Enabled</option> 418 <option value="true">Enabled</option>
488 </param> 419 </param>
489 <when value="true"> 420 <when value="true">
490 <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/> 421 <expand macro="input_files_all" format="@FORMAT@" label="FASTA/FASTQ file(s)" help="@HELP@"/>
491 <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."> 422 <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.">
492 <option value="true" selected="true">True</option> 423 <option value="true" selected="true">True</option>
493 <option value="false">False</option> 424 <option value="false">False</option>
494 </param> 425 </param>
495 </when> 426 </when>
496 <when value="false"/> 427 <when value="false"/>
497 </conditional> 428 </conditional>
498 </xml> 429 </xml>
499 430
500 <xml name="input_additional_files_paired" token_format="" token_label="" token_help="" > 431 <xml name="input_additional_files_paired" tokens="format" token_help="" >
501 <conditional name="additional_reads"> 432 <conditional name="additional_reads">
502 <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)."> 433 <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).">
503 <option value="false" selected="true">Disabled</option> 434 <option value="false" selected="true">Disabled</option>
504 <option value="true">Enabled</option> 435 <option value="true">Enabled</option>
505 </param> 436 </param>
506 <when value="true"> 437 <when value="true">
507 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/> 438 <expand macro="input_files_paired" format="@FORMAT@" label="FASTA/FASTQ file(s)" help="@HELP@"/>
508 </when> 439 </when>
509 <when value="false"/> 440 <when value="false"/>
510 </conditional> 441 </conditional>
511 </xml> 442 </xml>
512 443
522 <when value="value"> 453 <when value="value">
523 <param name="manual" type="float" min="0" value="" label="Set value"/> 454 <param name="manual" type="float" min="0" value="" label="Set value"/>
524 </when> 455 </when>
525 </conditional> 456 </conditional>
526 </xml> 457 </xml>
527 <xml name="pipeline_options"> 458 <xml name="pipeline_options" token_additional_help="">
528 <param name="mode_sel" type="select" label="Pipeline options" multiple="true" optional="true" display="checkboxes" help="Error correction requires FASTQ input files."> 459 <param name="mode_sel" type="select" label="Pipeline options" multiple="true" optional="true" display="checkboxes" help="Error correction requires FASTQ input files. @ADDITIONAL_HELP@">
529 <option value="--disable-rr">Disable repeat resolution (--disable-rr)</option> 460 <option value="--disable-rr">Disable repeat resolution (--disable-rr)</option>
530 <yield/> 461 <yield/>
531 </param> 462 </param>
532 </xml> 463 </xml>
533 <xml name="kmer" token_help="" token_default="21,33,55,77"> 464 <xml name="kmer" token_help="" token_default="21,33,55,77">
548 </param> 479 </param>
549 </when> 480 </when>
550 </conditional> 481 </conditional>
551 </xml> 482 </xml>
552 <xml name="nanopore_pacbio"> 483 <xml name="nanopore_pacbio">
553 <param argument="--nanopore" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="Nanopore reads" help="SPAdes will use Oxford Nanopore reads for gap closure and repeat resolution"/> 484 <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"/>
554 <param argument="--pacbio" type="data" format="fastq,fastq.gz" 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"/> 485 <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"/>
555 </xml> 486 </xml>
556 <xml name="flrna"> 487 <xml name="flrna">
557 <param argument="--fl-rna" name="flrna" type="data" format="fastq,fastq.gz,fasta,fasta.gz,fastqsanger,fastqsanger.gz" 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."/> 488 <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."/>
558 </xml> 489 </xml>
559 490
560 <xml name="phred"> 491 <xml name="phred">
561 <param argument="--phred-offset" type="select" label="Set Phred quality offset" help="Phred quality offset in the input reads. Default: auto-detect"> 492 <param argument="--phred-offset" type="select" label="Set Phred quality offset" help="Phred quality offset in the input reads. Default: auto-detect">
562 <option value="auto" selected="true">Auto</option> 493 <option value="auto" selected="true">Auto</option>
563 <option value="33">33 (Sanger)</option> 494 <option value="33">33 (Sanger)</option>
564 <option value="64">64 (Illumina)</option> 495 <option value="64">64 (Illumina)</option>
565 </param> 496 </param>
566 </xml> 497 </xml>
567 <xml name="reads" token_paramname="reads" token_help="" token_label=""> 498 <xml name="reads" token_paramname="reads" token_help="" token_label="">
568 <param name="@PARAMNAME@" type="data" format="fastq,fastq.gz" label="@LABEL@ reads" help="@HELP@"/> 499 <param name="@PARAMNAME@" type="data" format="@FASTQ_INTYPES@" label="@LABEL@ reads" help="@HELP@"/>
569 </xml> 500 </xml>
570 <xml name="sanger"> 501 <xml name="sanger">
571 <param argument="--sanger" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="Sanger reads"/> 502 <param argument="--sanger" type="data" format="@FASTQ_INTYPES@" multiple="true" optional="true" label="Sanger reads"/>
572 </xml> 503 </xml>
573 <xml name="contigs"> 504 <xml name="contigs">
574 <param argument="--trusted-contigs" type="data" format="fasta,fasta.gz" 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."/> 505 <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."/>
575 <param argument="--untrusted-contigs" type="data" format="fasta,fasta.gz" 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."/> 506 <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."/>
576 </xml> 507 </xml>
577 <xml name="assembly_graph"> 508 <xml name="assembly_graph">
578 <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."/> 509 <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."/>
579 </xml> 510 </xml>
580 <xml name="optional_output"> 511 <xml name="optional_output">